MES Systems Engineer

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.

About the Organization 

Lilly IT builds and maintains capabilities using cutting edge technologies like most prominent tech companies. What differentiates Lilly IT is that we create new possibilities through tech to advance our purpose – creating medicines that make life better for people around the world, like data driven drug discovery and connected clinical trials. We hire the best technology professionals from a variety of backgrounds, so they can bring an assortment of knowledge, skills, and diverse thinking to deliver innovative solutions in every area of our business. 

The Manufacturing and Quality Tech team leverages technology and analytics to transform and scale manufacturing to the digital plant of the future and support manufacturing operational excellence and productivity. This team helps produce medicines using machine learning and robotic capabilities with some of the most sophisticated manufacturing technologies and rigorous quality standards.

MES Systems Engineer:

The Tech@Lilly MQ team at the Indianapolis Parenteral Manufacturing site is actively looking for a System Engineer for Manufacturing Execution Systems (MES) to focus on Digital Transformation. Are you passionate about manufacturing excellence and applying technology to make reliable and life-saving medicines? If so, bring YOUR skills and talents to Lilly where you’ll have the chance to create an impact on the lives of patients with “Safety First and Quality Always”.

What You’ll Be Doing: 

As an MES System Engineer, you will play a key role in supporting and evolving manufacturing execution systems at the Indy Parenteral Manufacturing (IPM) site. You will work closely with cross‑functional partners to understand manufacturing processes and translate them into system requirements, electronic Master Batch Records (MBRs), and MES solutions that meet quality, compliance, and operational needs.

In the near term, this role will support our current MES platform, PMX, including design, configuration, validation, deployment, and ongoing support of electronic MBRs and related MES functionality. Looking ahead, you will also contribute to the site’s digital transformation, helping to plan and execute the transition to PharmaSuite, our next‑generation MES platform.

You will be involved throughout the solution lifecycle—from requirements gathering and system design to testing, validation, and production support—while driving MES solution integration with broader manufacturing, warehouse, and IT systems. This role offers exposure to critical projects that directly impact our ability to safely and reliably manufacture medicines for patients around the world.

This is an excellent opportunity to grow technical and business skills, contribute to meaningful manufacturing outcomes, and be part of a team driving continuous improvement and operational excellence at IPM.

How You’ll Succeed: 

• Design, configure, and support MES and Digital Execution solutions that enable safe, efficient pharmaceutical manufacturing.
• Provide hands‑on technical support for manufacturing systems, including MES, automation, and supporting IT infrastructure, helping to quickly diagnose and resolve issues that impact operations.
• Troubleshoot equipment, software, and network‑related issues to minimize downtime and support reliable production.
• Partner closely with Engineering, Operations, Quality, and IT to investigate issues, identify root causes, and implement sustainable solutions.
• Contribute to the design of integrated, scalable, and user‑friendly MES solutions, ensuring systems work seamlessly across manufacturing and digital platforms.
• Apply technical expertise to translate business and manufacturing needs into practical system designs and configurations.
• Incorporate security, data integrity, and compliance considerations into system designs to protect company data and meet regulatory expectations.
• Communicate technical concepts clearly to both technical and non‑technical stakeholders, supporting informed decision‑making.
• Build a strong understanding of IPM manufacturing processes and use that knowledge to support and improve operational workflows.
• Support adoption of new and existing digital solutions by working with business SMEs and aligning with site and IT strategies.
• Collaborate with global and local technical experts to help shape solution direction and balance usability, performance, and maintainability.
• Participate in the review and approval of validation and lifecycle documentation (e.g., SOPs, protocols, and system records) to support compliant system delivery 

What You Should Bring: 

• Experience supporting Manufacturing Execution Systems (MES), such as PMX and/or PharmaSuite, with the ability to translate manufacturing needs into system requirements, configurations, and electronic batch record (eMBR) updates.
• Exposure to or interest in supporting MES platform transitions, including learning and contributing to PMX → PharmaSuite migration activities in a phased manufacturing environment.
• Experience in computer system validation (CSV) activities, including test execution and documentation, with an understanding of data integrity expectations in a regulated environment.
• Ability to help gather and document non‑functional requirements (performance, security, usability, data integrity, reliability) and work collaboratively with other MES engineers or architects to implement solutions that meet those needs.
• Hands‑on troubleshooting skills for MES‑related issues, including application behavior, system interfaces, and connectivity, with a collaborative approach to identifying root causes and reducing production downtime.
• Strong collaboration skills and experience working with cross‑functional teams such as Operations, Engineering, Quality, and IT to support adoption and sustained use of digital manufacturing solutions.
• Awareness of secure and compliant system use, including following access, security, and data protection practices in regulated manufacturing systems.
• Exposure to reporting, dashboards, or manufacturing data flows, with the ability to support data continuity as systems modernize.
• Experience supporting project execution through task tracking, status updates, and coordination within a defined workstream or project team.
• Curiosity and a growth mindset, with an interest in learning new technologies and manufacturing digital trends to continuously improve system reliability and execution.
• Clear communication skills, with the ability to explain technical concepts to both technical and non‑technical partners and document work in a concise, understandable way.

Basic Qualifications: 

• Bachelors in IT, Science, Technology Engineering, or related field.
• 1+ years of IT experience, software engineering, and/or digital capabilities, specifically experience working with Pharmaceutical Manufacturing Execution Systems, specifically PMX, PharmaSuite, PAS-X, and/or Syncade as well as WES/SAP.
• Experience supporting/developing IT applications/solutions.
• Hands-on experience with manufacturing operations and Manufacturing Execution Systems (MES), including implementation, integration, support, or optimization in a manufacturing environment.
• Qualified applicants must be authorized to work in the United States on a full-time basis. Lilly will not provide support for or sponsor work authorization or visas for this role, including but not limited to F-1 CPT, F-1 OPT, F-1 STEM OPT, J-1, H-1B, TN, O-1, E-3, H-1B1, or L-1

Preferred Qualifications:

• Experience working in a GXP, regulated environment.
• Experience maintaining Computer Systems Validation in line with pharmaceutical computer system quality regulations (e.g. cGMP’s, FDA 21 CFR Part 11) and other applicable regulations (e.g. privacy, OSHA, etc.)

Additional Information: 

• Position based in Indianapolis, Indiana
• 8-hour days, possible after-hour support
• On site presence minimum 4 days a week
• Occasional travel may be required.
• Must maintain a safe work environment, working safely and accountable for supporting all health and safety corporate and site goals. 

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 Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

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

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.

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