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Eli Lilly and Company

Sr Principal Engineer - MES

United States

The anticipated wage for this position is $129,000 - $189,200

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Job details

Pay: The anticipated wage for this position is $129,000 - $189,200
Experience: Experience: 8+ years of experience in MES
Posting language: English
Posted: Oct 29, 2026

Original job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work - but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.

This is an opportunity you don’t want to miss! Lilly is entering an exciting period of growth, and we are committed to delivering innovative medicines to patients around the world. Lilly is investing to create several new state-of-the-art manufacturing sites. These brand-new facilities will utilize the latest technology for API Manufacturing and will include several platforms including Vaccines, Radio Therapy and Gene Therapy Drug Substance Manufacturing. This is an exciting once-in-a-lifetime opportunity to help build and operate a new site. These new API sites will be built using the latest high-tech equipment, advanced highly integrated and automated manufacturing systems, and have a focus on minimizing the impact to our environment.

What You’ll Be Doing:

You will be part of Tech at Lilly MQ (Manufacturing and Quality), an organization that drives manufacturing operational excellence and productivity efforts through utilization of technology. Tech at Lilly MQ strives to enable the making of medicine “with safety first and quality always”.

The MES Sr Principal Engineer will play a crucial role in delivering the Manufacturing Execution Systems through common modules that enable manufacturing sites to deliver world class performance. The role encompasses responsibility for both the architectural and technical components of the Manufacturing Execution Systems (MES) solution. This involves providing expert guidance and oversight in the design, implementation, and optimisation of MES architecture to ensure it aligns with the organisation’s strategic objectives and operational requirements. A key part of the role is to establish and maintain the direction for Solution Architecture in collaboration with the global Group. This includes implementing defining standards, best practices, and technical frameworks that steer the development and evolution of the MES modules, ensuring consistency, scalability, and reliability across all manufacturing sites.

How You’ll Succeed:

Utilizes solid understanding of Manufacturing and Quality business processes to anticipate MES short term and future needs from an IT Architecture standpoint.
Works with global Architects, Enterprise Architects, local IT teams and other global teams to identify solutions to complex problems related to MES.
Sets direction through the formation of a strategic roadmap and evolution of the site design for API MES solution and systems interfaced to MES.
Collaborates, influences and/or leads the definition of global IT support and/or delivery processes.
Provides deep technical knowledge, monitors solution delivery projects for compliance with the defined reference architecture and proposes and facilitates proof-of-concepts to enable clarity around future state direction.
Collaborates with Enterprise Architects to research, identify, test, certify, select and introduce innovative technology products required for solution development and delivery.
Collaborates with the Data Management teams to ensure understanding of, and alignment with Data Architecture Standards
Actively collaborates with Cybersecurity and Protect Lilly teams to introduce operating principles for MQ IDS MES systems, interfaces and architecture (e.g. proper patching process, LCM, software version control).
Ensure IT vendors understand the Cyber Security and Protect Lilly requirements and are able to translate these into implementation specifications.
Acts as interface between IT and Business Partners on (or across) large projects and programs from a technical perspective (e.g. reporting, archival, performance, MES scope expansions).
Keeps outward focus to identify new trends and opportunities.
Keeps relationships with other large Pharma companies to ensure Lilly roadmap and decisions are in line and competitive with industry trends.
Acts as coach/mentor of global and local MES team members and others regarding technologies, architecture and technical design as appropriate.
Leads and/or supports development of business cases related to MES.
Proactively influence the business to drive value and implement the appropriate technical solutions
Find innovative ways to leverage MES to drive business value

Basic Requirements:

Education: Bachelor’s degree in Computer Science, Engineering or related field
Experience: 8+ years of experience in MES
Knowledge: Strong knowledge with distributed S95 Level 3 solutions, commercial configurable software (COTS) suppliers, and business intelligence. Strong technical Skills: including infrastructure, interfaces and configuration capabilities
Experience in Pharma and GMP Manufacturing

Additional Preferences

Experience: Experience managing programs/projects in the pharmaceutical business. Previous experience in the startup of a new facility or clinical development manufacturing site.
Skills: Strong analytical and problem-solving skills, with the ability to assess risks, manage trade-offs, and make sound decisions. Excellent communication and leadership skills to interact with stakeholders at all levels of the organization
Leadership Skills: Proven leadership experience in managing cross-functional teams.
Industry Engagement: Active participation in industry forums and standards organizations.
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Other Information:

Role is Monday through Friday and based on-site. Must be flexible in providing support to accommodate other inputs (production schedules, shutdowns, etc.). Occasional extended hour and / or off-hour work may be required.
Roles will be based in Indianapolis IN,

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is $129,000 - $189,200

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

#WeAreLilly

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More about this job

Skills

MES
Business processes
Regulatory compliance
Research
Data management
Architecture regulations
Cybersecurity
IDS
Reporting
Computer science
Business intelligence
Good manufacturing practices
Problem solving
Communication skills
Leadership

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