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Jefferies 2015 Global Healthcare Conference June 2015

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SAFE HARBOR PROVISIONS FOR FORWARD-LOOKING STATEMENTS: This news release may contain forward-looking statements within the meaning of the federal securities laws. Statements regarding future events, developments, the Company's future performance, as well as management's expectations, beliefs, intentions, plans, estimates or projections relating to the future (including, without limitation, statements concerning revenue and net income), are forward-looking statements within the meaning of these laws and involve a number of risks and uncertainties. Management believes that these forward looking statements are reasonable and are based on reasonable assumptions and forecasts, however, undue reliance should not be placed on such statements that speak only as of the date hereof. Moreover, these forward-looking statements are subject to a number of risks and uncertainties, some of which are outlined below. As a result, actual results may vary materially from those anticipated by the forward-looking statements. Among the important factors that could cause actual results to differ materially from those indicated by such forward-looking statements are: the volume and timing of systems sales and installations; length of sales cycles and the installation process; the possibility that products will not achieve or sustain market acceptance; seasonal patterns of sales and customer buying behavior; impact of incentive payments under The American Recovery and Reinvestment Act on sales and the ability of the Company to meet continued certification requirements; the development by competitors of new or superior technologies; the timing, cost and success or failure of new product and service introductions, development and product upgrade releases; undetected errors or bugs in software; product liability; changing economic, political or regulatory influences in the health-care industry; changes in product-pricing policies; availability of third-party products and components; competitive pressures including product offerings, pricing and promotional activities; the Company's ability or inability to attract and retain qualified personnel; possible regulation of the Company's software by the U.S. Food and Drug Administration; uncertainties concerning threatened, pending and new litigation against the Company including related professional services fees; uncertainties concerning the amount and timing of professional fees incurred by the Company generally; changes of accounting estimates and assumptions used to prepare the prior periods' financial statements; general economic conditions; and the risk factors detailed from time to time in the Company’s periodic reports and registration statements filed with the Securities and Exchange Commission.

Safe Harbor Provisions

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Quality Systems, Inc. and its NextGen Healthcare subsidiary develop and market computer-based practice management, electronic health records (EHR) and revenue cycle management applications, as well as connectivity products and services, for medical and dental group practices and small hospitals.

• Revenue primarily derived from physician group businesses that utilize

the Company’s high functionality practice management suites • Focus is on growing organically with a strong emphasis on reinvestment

in new product and service development initiatives • Acquisitions of complementary business lines are also key drivers of

growth

Company Overview

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Organizational Timeline

A willingness to reinvest and reinvent to better compete

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Quality Systems Today

March 31st, 2015 TTM Revenue: $490.2mm Non-GAAP EPS: $0.62

TTM Revenue: $373.8mm

(76% of total) ~ 85,000 Providers

Markets Served:

Ambulatory Practices

• Practice

Management • EHR • Population Health

Management • Patient Portal

TTM Revenue: $18.5mm

(4% of total) ~10,000 Dentists

Markets Served:

Dental Practices • Practice

Management • Electronic

Dental Records

TTM Revenue: $80.0mm

(16% of total) ~ 6,500 Providers

Markets Served:

Ambulatory Practices

• Revenue Cycle

Management • Other Services

TTM Revenue: $18.0mm

(4% of total) ~ 300 Hospitals

Markets Served:

Small Hospitals • Financials • Clinical • Surgery

Scheduling

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Market Drivers

• American Recovery and Re-investment Act (ARRA) – 2/09 – Over $60 billion in incentive and grant money to stimulate

healthcare information technology (HIT) adoption. – Stringent rules for providers to qualify for funds known as

“Meaningful Use” – First time that state-based Medicaid programs and Departments

of Health become major purchasers of HIT • Pay-for-performance (P4P) programs, patient-centered

medical home, and other quality initiatives • Consumerism and Personal Health Records (PHR) • Interoperability and community-based data exchange

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Medicare Complete EHR EP Attestations Top Ten Vendors

9,204

16,727

17,104

21,070

29,527

38,541

47,185

51,876

66,498

152,888

- 20,000 40,000 60,000 80,000 100,000 120,000 140,000 160,000 180,000

Community Computer Service Inc

McKesson

Practice Fusion

athenahealth, Inc

Greenway Health

GE Healthcare

NextGen Healthcare

eClinicalWorks LLC

Allscripts

Epic Systems Corporation

Based on ONC March 2015 attestation data

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Medicare Complete EHR EP Attestations: Top Five vs. Top Ten Vendors by % Total

The top five vendors continue to dominate more than half (53%) of all attestations, where “All Other” represents a collection of almost 500 additional vendors

Based on ONC attestation data March 2015

22.9%

9.9%

7.8%

7.1%

5.8%

4.4%

3.2% 2.6%

2.5% 1.4%

32.6%

Epic Systems Corporation

Allscripts

eClinicalWorks LLC

NextGen Healthcare

GE Healthcare

Greenway Health, LLC

athenahealth, Inc

Practice Fusion

McKesson

Community Computer Service, Inc

All Other

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Hospital Top 10 Vendors

Vendor Attestations % Total 1 Epic Systems Corporation 1,414 17.7% 2 MEDITECH 1,357 17.0% 3 CPSI 1,234 15.5% 4 Cerner Corporation 943 11.8% 5 McKesson 656 8.2% 6 MEDHOST 606 7.6% 7 Healthland, Inc. 565 7.1% 8 Allscripts 332 4.2% 9 NextGen Healthcare 153 1.9% 10 Health Care Systems Inc 119 1.5%

All Other 7.4%

Based on ONC March 2015 attestation data

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Hospital Attestations: Top Ten Vendors by % Total

Based on ONC March 2015 attestation data

17.7% 17.0%

15.5%

11.8%

8.2%

7.6%

7.1%

4.2%

1.9% 1.5%

7.4%

Epic Systems Corporation

MEDITECH

CPSI

Cerner Corporation

McKesson

MEDHOST

Healthland, Inc.

Allscripts

NextGen Healthcare

Health Care Systems, Inc.

All Other

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EHR Incentive Program

Stage 1 Payments Active Registrations Providers Paid Dollars Paid Medicare Eligible Professionals 353,350 290,304 $7.67 Billion Medicaid Eligible Professionals 177,406 139,110 $3.63 Billion

Eligible Hospitals & CAHs 4,811 4,793 $18.31 Billion

Total 535,567 434,207 $29.61 Billion

Stage 2 Payments Providers Paid Dollars Paid Medicare Eligible Professionals 38,472 $254.66 Million Eligible Hospitals 1,440 $1.08 Billion

Total 39,912 $1.33 Billion

Total Dollars Paid $30.93 Billion

Total Program to Date

Based on ONC March 2015 attestation data

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Market Opportunity & Positioning

Population Health Management

$45 Billion

19% Penetrated

Penetration Opportunity High Opportunity (Low Penetration) Low Opportunity (High Penetration)

Gro

wth

H

igh

Gro

wth

Revenue Cycle Management Services

$26 Billion

20-25% Penetrated

Low

Gro

wth

Ambulatory Software

$13 Billion

60-70% Penetrated

<100 Bed Hospital Software

$3 Billion

60-70%

Penetrated

Dental Software $1 Billion

80%

Penetrated

1. Citi Research, Oliver Wyman Analysis, 2. TriZetto, Industry Perspectives on Future Trends in Population Health; 3: KPMG Population Health Investment Survey

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Representative Customers

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Strategic Dial Movers

Continued Growth of Our Core Businesses • This is the fourth year of government incentive payments to

physicians and hospitals with half of the market to go • Stage 1-2-3 – Resale Market • ICD 9-10-11 – Resale Market • Healthcare Reform • Five Years of Incentives • Five Years of Penalties • 10 Year Adoption Period

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Strategic Dial Movers

Focusing on Opportunities to Sell Complementary Products • There is significant opportunity in cross-selling new

solutions to the existing customer base and bundling multiple solutions for new customers

• Large Installed Base ~ 85,000 providers ~ 10,000 dentists ~ 300 hospitals

• Four Divisions 28 Product & Service Offerings

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95% 91%

12% 2%

67%

6% 18%

5% 9%

88% 98%

33%

94% 82%

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

PM EHR RCM Mirth Patient Portal Population Health Dashboard

Product Penetration

Product Penetration in Current Client Base

• Creating demand for ancillary products • Focused on client education, product bundling, and marketing • Client base demand for products is significant

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Reorganized Functional Areas

Research & Development

Sales & Marketing

Finance & Back Office

Operations

Implementation & Professional

Services

Information Technology

Services

• Reorganized functional areas to maximize efficiencies company-wide:

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Accountable Care Organizations

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Strategic Dial Movers

Expand Revenue Cycle Management Capabilities • NextGen RCM has been set-up to grow the company’s RCM

business and is already seeing strong results. • Reform Provides the Fuel • Core vs. Non-Core Competency • Reimbursement Pressure – Revenue Down • Regulatory Pressure – Costs Up

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Quick Fact

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Majority of Practices See Results (with RCM)

Source: MGMA. Medical Billing Services Information Exchange: #4840. Based on MGMA Survey: Medical Billing Companies Produce Strong Results, 2009. (http://www.mgma.com/store/Books/Medical-Billing-Services/)

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Revenue Cycle Management is a $50 Billion Market in the United States

• Revenue cycle management (RCM) is currently a $50 billion market in the US

7.5 Times Larger than the EHR Market

Source: Frost & Sullivan 2013

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Strategic Dial Movers

Continued Growth through Acquisitions • QSI is focused on “bolt-on” acquisitions to fill a strategic gap or kick-start entry into newer business lines

• Eleven Acquisitions in Last Seven Years • RCM • Analytics • Patient Management • Regulatory and Clinical Reporting Tools

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Strategic Dial Movers

Expand Offshore Capabilities to Capture Cost Efficiencies • A growing technology innovation center in Bangalore, India

currently employs more than 375 technologists and engineers

• Opened in July 2011 • Now full service R&D shop

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The Mirth Plan

Headquartered in Costa Mesa, CA 100+ employees • Experts in Healthcare Data

Integration and Health Information Exchange

• Global leader in commercial and open source software for Health IT

• Focused exclusively on healthcare software for 14 years

• Revolutionizing how organizations adapt to evolving HIT requirements and push towards interconnected healthcare

• Family of Mirth products connect seamlessly and naturally within the HIT ecosystem

• Solution to satisfy demands from HIEs and the emergence of ACOs

Software Development

Healthcare Focus

Mirth Products

1993 1999 2006

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The Mirth Solution

Mirth Results • Central Data Repository • Document Factory (C-CDA) • Provider Portal • IHE: PIX/PDQ, XDS.b, etc • Consent & Confidential Info Mirth Mail • Secure Direct Messaging, Chat, &

Provider Directory Mirth Care • Chronic Disease Management & Care

Management Mirth Match • EMPI & Record Locator Service Mirth Connect • Data Integration Engine Mirth Analytics • Business Intelligence, Reporting, &

Analytics

HL7, DiCOM, X12, CCD, C-CDA, EHR Integration

Direct Messaging, Secure Chat, HPD+ Provider Directory

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Financial Highlights

Fiscal year ended March 31 2015 2014 2013 2012 2011

Revenue $490,225 $444,667 $460,229 $429,835 $353,363

Net income* $27,332 $33,022 $59,124 $75,657 $61,606 Non-GAAP diluted earnings per share ** $0.62 $0.70 $1.14 $1.37 $1.15 Cash dividends declared per share $0.70 $0.70 $0.70 $0.70 $0.63

Total Shareholders’ Equity $283,540 $295,090 $307,050 $295,177 $224,670

(in thousands, except per share amounts)

*2014 Net Income excludes $26 million impairment charge and estimated tax impact, 2013 Net Income excludes $17.4 million impairment charge and estimated tax impact of such charge **2012 and 2011 Non-GAAP Diluted Earnings per Share are estimated as they were not formally announced in those years

A proven record of delivering value back to Shareholders

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Recurring Service Revenue as Percentage of Total Revenue

60%

65%

70%

75%

80%

85%

* Recurring service revenue consists of maintenance, EDI, RCM and other services.

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Why Quality Systems?

Proven Growth and Profitability

• Proven track record of organic growth – Five-year revenue CAGR of 9% – Self-funded, highly profitable growth strategy – Recurring revenue represented 83% of total revenue in FY 2015 – Cash and marketable securities of $130.6 million and no debt

Substantial Customer Base

• Over 4,400 clients representing ~ 95,000 providers • ~ 300 hospital relationships

Leading Suite of HCIT Products • Certified technology platform in hospital, physician and dental markets

Positive HCIT Industry Trends

• Increasing focus on technology benefits in healthcare • Healthcare Reform • Economic Stimulus Package/Obama Plan from U.S. Government

Experienced Management Team

• Extensive years of experience and working collaboratively as a management team

Robust Sales Pipeline • $161.3 million NextGen Healthcare sales pipeline @ 5/21/15 • Lead Generation up year over year

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18111 Von Karman Avenue Suite 700 Irvine, California 92612 (949) 255-2600 Phone www.qsii.com www.nextgen.com Susan Lewis Investor Relations slewis@qsii.com

Steven T. Plochocki Chief Executive Officer splochocki@qsii.com

Daniel J. Morefield Chief Operating Officer dmorefield@qsii.com John Stumpf Interim Chief Financial Officer jstumpf@qsii.com