Clinical Analyst Jobs in Boston, MA
Clinical Analyst jobs in Boston are in strong demand, concentrated in the Longwood Medical Area, Seaport District, and downtown Financial District across healthcare, health IT, and biopharma. Employers hiring right now include Medpace, Piper Companies, and Takeda Pharmaceuticals. Scan the live roles below and apply to whichever ones fit.
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Location: Boston (Hybrid)
Organization Summary:
Community Care Cooperative (C3) is a 501(c)(3) non-profit, Accountable Care Organization (ACO) governed by Federally Qualified Health Centers (FQHCs). Our mission is to leverage the collective strengths of FQHCs to improve the health and wellness of the people we serve. We are a fast- growing organization founded in 2016 with 9 health centers and now serving hundreds of thousands of beneficiaries who receive primarycare at health centers and independent practices across Massachusetts. We are an innovative organization developing new partnerships and programs to improve the health of members and communities, and to strengthen our health center partners.
Job Summary:
The Analyst II, Ambulatory Clinical position will be housed under a subsidiary organization of C3, Community Technology Cooperative, LLC (CTC) to implement, maintain, support, and maximize the use of clinical, financial, and administrative portions of the software applications utilized by CTC in conducting daily operations under the direction of the Director of Clinical Applications.
Responsibilities:
- Maintain current clinical, financial, and administrative applications, implementing new clinical, financial, and administrative Epic applications
- Assist in the assessment of workflow processes and assisting in process re- engineering to achieve efficiencies in departmental operations
- Assist users in developing reports and analyses, troubleshooting, and resolution of application issues
- Work with the IT Education staff to assist in training users and in the development of documentation
- Maintain a level of knowledge about IT operations and network issues and maintaining current industry knowledge
- Ability to maintain current system applications
- Facilitate end users’ ability to understand and maximize the use of the software to perform daily operations
- Evaluate user knowledge and work with IT education staff to develop specialized training when necessary; educate users in system optimization
- Acts as liaison between users and the software vendor(s)
- Guides the modification of system applications in instances where current applications impede performance or where changes will enhance performance
- Ensure system application updates are working properly before updates are loaded into the live system by coordinating testing and update dates with users and vendors
- Integrate new application(s) in the existing HIS according to the implementation schedule
- Respond to user questions with timely answers and/or referral to appropriate department/person
- Assist users with technical problems by alerting HIS Operations staff to the need for repair or investigation
- Coordinate with Database Analysts to provide expertise in the development of reports and analyses
- Work with other IT staff to ensure interfaces between applications and systems are functioning properly
- Maintain and periodically review dictionaries, assist in entering and maintaining user codes, maintain the security of applications, and ensure consistency between various dictionaries
- Investigate on timely basis discrepancies in statistics which could indicate a problem with the accuracy of data
- Work with application managers, staff from affected areas, and representatives from other impacted areas, to analyze computer system functions and compare data and existing systems both functionally and procedurally
- Implement new clinical, financial, and administrative software, including add-on features, and/or new routines in existing applications
- Participates with other IT staff and other clinical, financial, and administrative areas in the planning and implementation stages of the application, including the development of dictionaries
- Work with Department Managers and IT Education staff to ensure training programs for use of applications are developed and conducted for all levels of users and participate in such programs when needed
- Develop system documentation to supplement vendor manuals and which defines processes, procedures, and policies regarding utilization of various functions
- Assist departments with the development of downtime procedures
- Work with Operation Manager and staff to establish schedules for report production and system jobs to maintain balanced system utilization and minimize system degradation, if necessary
- Sustain working knowledge of key functions of all aspects of the department in order to provide emergency coverage in the absence of others in the department
- Work with Applications Manager to accomplish other departmental tasks
- Notify the Applications Manager of requests for custom modifications to standard applications and of any updates to standard systems which replace existing custom modifications so that the Application Manager can take appropriate action
- Assist in the development of IT policies and procedures and notify users as appropriate
- Participate in applications on-call rotation for the information system
- Participate in hospital quality teams and committees as necessary
- Demonstrates competent and effective job performance skills as evidenced by the volume, skill, and technical knowledge of work performed, neatness, accuracy, thoroughness, and completeness, and the ability to follow instructions
- Demonstrates the ability to interact effectively and in a professional manner with peers
- Administration and other customers as demonstrated by willingness to work with others to achieve CTC’s goals
- Ability to present a friendly and positive manner, willingness to seek additional tasks
- Responsibility to assist the department and/or peers, ability to be flexible and perform new tasks and adjust to change even under pressure
- Ability to accomplish results by working effectively with or through other people
- Ability to hear and communicate with others in a clear, understandable, and professional manner in person and on the phone
- Demonstrated use of good written and verbal communication skills
- Maintain current industry knowledge by attending industry seminars, reviewing professional literature, and communicating on a regular basis with other IT analysts
- Other duties as assigned
Required Skills:
- Ability to understand, analyze, document, and explain business processes and the data that underly them
- Experience working with Electronic Health Records, medical claims, and other healthcare data
- Flexible and adaptable to change in a fast-paced environment
- Demonstrated ability to work both independently and as part of a team
- Demonstrated ability to thrive in a fast-past environment
- Nuanced interpersonal communication skills
- Weekly on-call will be a requirement for this position
Desired Other Skills:
- Familiarity with the MassHealth ACO program
- Familiarity with Federally Qualified Health Centers
- Experience working in a provider organization
- Experience working in a managed care environment
- Experience with anti-racism activities, and/or lived experience with racism is highly preferred
Qualifications:
- Bachelor’s degree in a healthcare-related field, Information Systems or Business Management
- Preferred Epic application proficiency, physician builder or connect builder certification but not required
- Minimum of 2 year's experience working within Epic applications
- Prior EHR systems support preferred
** In compliance with Control practices per Mass.gov recommendations, we require all employees to be vaccinated consistent with applicable law. **
See All 22 Clinical Analyst Jobs in Boston
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Find Clinical Analyst JobsClinical Analyst Job Market in Boston
Who's Hiring
- Medpace3

- Piper Companies2

- Takeda Pharmaceuticals2

- Vertex Pharmaceuticals2

- Community Care Cooperative2

Top Industries Hiring
- Healthcare & Medical Services6
- Science & Research5
- Staffing & Recruiting3
- Medical Devices2
- Biotechnology & Pharmaceuticals2
Clinical Analyst Jobs in Boston: Frequently Asked Questions
How do I get a clinical analyst job in Boston?
Boston's strongest hiring comes from the hospitals and research institutions clustered in Longwood, the health IT companies headquartered in the Seaport, and the biopharma firms along Route 128 and in Kendall Square. Candidates with EHR platform experience, particularly Epic or Cerner, and a background in clinical workflows stand out. Targeting academic medical centers and health system vendors gives you the widest pool of openings in this city.
Which companies hire clinical analysts in Boston?
Boston clinical analyst roles are posted by Medpace, Piper Companies, and Takeda Pharmaceuticals and others right now, based on current listings on Migrate Mate as of June 2026. Boston's mix of large academic medical systems, regional health plans, and venture-backed digital health startups means openings appear across employer sizes and sectors year-round.
Are there remote clinical analyst jobs in Boston?
Yes, though availability depends on the role: analysts focused on data, reporting, and system configuration tend to work remotely, while those supporting active clinical operations or go-live implementations are usually on-site. About 73% of clinical analyst openings tied to Boston are remote or hybrid as of June 2026. Health IT vendors and payer-side analytics teams in Boston offer the most consistent remote options.
How can I get a clinical analyst job in Boston with little or no experience?
The most realistic entry path in Boston is through health IT consulting firms and staffing agencies that place analysts at major hospital systems for go-live and optimization projects. Boston-area academic medical centers also hire clinical informatics coordinators and application analysts at the associate level. Certifications in Epic or a related EHR platform, even without years of clinical experience, consistently open doors with Longwood-area employers and regional health plans.
Which industries hire the most clinical analysts in Boston?
Boston clinical analyst roles concentrate in Healthcare & Medical Services, Science & Research, and Staffing & Recruiting, based on current listings on Migrate Mate as of June 2026. Boston's density of research hospitals, health insurance carriers, and biopharma companies makes it one of the most active markets in the country for this role.
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