Jefferies 2015 Global Healthcare Conference June 2015

1 Safe Harbor Provisions

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.

2 Company Overview

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

3 Organizational Timeline

A willingness to reinvest and reinvent to better compete

4 Quality Systems Today

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

TTM TTM TTM TTM $18.5mm Revenue: $373.8mm Revenue: Revenue: $80.0mm Revenue: $18.0mm (76% of total) (4% of total) (16% of total) (4% of total)

~ 85,000 Providers ~10,000 Dentists ~ 6,500 Providers ~ 300 Hospitals

Markets Ambulatory Markets Dental Markets Ambulatory Markets Small Hospitals Served: Practices Served: Practices Served: Practices Served: • Financials • Practice • Practice • Revenue Cycle • Clinical Management Management Management • Surgery • EHR • Electronic • Other Services Scheduling • Population Health Dental Records Management •

5 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

6 Medicare Complete EHR EP Attestations Top Ten Vendors

Epic Systems Corporation 152,888

Allscripts 66,498

eClinicalWorks LLC 51,876

NextGen Healthcare 47,185

GE Healthcare 38,541

Greenway Health 29,527

, Inc 21,070

Practice Fusion 17,104

McKesson 16,727

Community Computer Service Inc 9,204

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

Based on ONC March 2015 attestation data

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

22.9%

9.9% Corporation Allscripts eClinicalWorks LLC

7.8% NextGen Healthcare GE Healthcare Greenway Health, LLC athenahealth, Inc 7.1% Practice Fusion

32.6% McKesson 5.8% Community Computer Service, Inc All Other 4.4%

3.2% The top five vendors continue to 2.6% dominate more than half (53%) of 1.4% 2.5% all attestations, where “All Other” represents a collection of almost 500 additional vendors Based on ONC attestation data March 2015

8 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 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

9 Hospital Attestations: Top Ten Vendors by % Total

17.7% 17.0% Epic Systems Corporation MEDITECH CPSI 7.4% Cerner Corporation McKesson 1.5% MEDHOST 1.9% 15.5% Healthland, Inc. 4.2% Allscripts NextGen Healthcare 7.1% Health Care Systems, Inc. All Other 11.8% 7.6% 8.2%

Based on ONC March 2015 attestation data

10 EHR Incentive Program

Total Program to Date

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 Total Dollars Paid Eligible Hospitals 1,440 $1.08 Billion $30.93 Billion Total 39,912 $1.33 Billion

Based on ONC March 2015 attestation data

11 Market Opportunity & Positioning

Revenue Cycle Population Health Management Services Management

Growth High $26 Billion $45 Billion <100 Bed 20-25% Penetrated 19% Penetrated Hospital Software

$3 Billion Ambulatory

Growth 60-70% Software Penetrated $13 Billion 60-70% Penetrated $1 Billion Growth Low 80% Penetrated

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

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

12 Representative Customers

13 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

14 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

15 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

100% 5% 9% 90% 33% 80%

70%

60% 82% 88% 94% 50% 98% 95% 91% 40% 67% 30%

20%

10% 18% 12% 2% 6% 0% PM EHR RCM Mirth Patient Portal Population Health Dashboard

Product Penetration

16 Reorganized Functional Areas

• Reorganized functional areas to maximize efficiencies company-wide:

Research & Development

Sales & Marketing

Finance & Back Office Operations

Implementation & Professional Services

Information Technology Services

17

Accountable Care Organizations

18 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

19 Quick Fact

20 Majority of Practices See Results (with RCM)

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

21 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

22 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

23 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

24 The Mirth Plan

Headquartered in Costa Mesa, CA 1993 1999 2006 100+ employees Software Healthcare Mirth Development Focus Products • 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

25 The Mirth Solution

Mirth Results Direct Messaging, • Central Data Repository Secure Chat, HPD+ Provider Directory • 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 HL7, DiCOM, X12, CCD, C-CDA, EHR Integration • Business Intelligence, Reporting, & Analytics

26 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

27 Recurring Service Revenue as Percentage of Total Revenue

85%

80%

75%

70%

65%

60%

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

28 Why Quality Systems?

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

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

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

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

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

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

29 18111 Von Karman Avenue Steven T. Plochocki Suite 700 Chief Executive Officer Irvine, California 92612 [email protected]

Daniel J. Morefield (949) 255-2600 Phone Chief Operating Officer www.qsii.com [email protected] www.nextgen.com John Stumpf Susan Lewis Interim Chief Financial Officer Investor Relations [email protected] [email protected]

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