Best Practices for Clinical Trial Budgeting

Episode Overview: Best Practices for Clinical Trial Budgeting

Clinical trial budgeting remains one of the biggest bottlenecks in study startups. Despite years of experience across sponsors, CROs, and research sites, budget negotiations are still plagued by delays, unclear justifications, misaligned expectations, and inefficient communication pathways.

In this special episode of the Clinical Trial Podcast, recorded live at Research Revolution, a clinical research conference hosted by Florence Healthcare. We take a hard look at why clinical trial budgeting continues to break down and what can be done to fix it.

This episode goes beyond surface-level complaints and gets into the real drivers of delay, including sponsor and CRO responsiveness, escalation failures, inconsistent terminology, and the lack of clear, data-driven budget justification.

What you’ll learn in this episode

In this conversation, we explore:

• The most common causes of delays during budget negotiations between sponsors and sites
• How sites can create clear, defensible budget justifications without triggering endless revision cycles
• What sponsors actually look for when approving higher-than-expected line items
• Best practices for internal rate cards, fee schedules, and budgeting templates
• How improved communication and transparency can reduce negotiation friction and cycle time

Featured guests

This episode features insights from three leaders who approach clinical trial budgeting from different vantage points:

Kristen McKenna, Senior Manager and Investigator Contracts Lead at Pfizer, oversees global site budgeting and contracting across large-scale clinical programs and shares sponsor-side perspectives on efficiency, compliance, and risk mitigation.

Heidi Castle, Director of Business Development at Mercy Research, brings more than a decade of experience across site operations, billing compliance, and budget negotiations, offering a pragmatic, site-focused view of operational realities.

Matt Lowery, CEO and Principal Consultant at The Pathways Group, has over 18 years of experience across site and sponsor roles and works directly with research sites on budget negotiation strategy, financial audits, and operational sustainability.

Who this episode is for

If you’re involved in clinical trial budgeting, contracting, or study startup – whether at a sponsor, CRO, or research site – this episode provides practical, experience-driven insights you can apply immediately.

Who this episode is for

If you’re involved in clinical trial budgeting, contracting, or study startup – whether at a sponsor, CRO, or research site – this episode provides practical, experience-driven insights you can apply immediately. 

Selected Links from the Episode:

• Florence Healthcare
• Research Revolution
• Pfizer
• Mercy Research
• The Pathways Group
• CPT Codes and Medicare Billing Guidance

Books:

• Nice Girls Don’t Get the Corner Office – Lois P. Frankel (Amazon, Barnes & Noble)
• Exactly What to Say – Phil M. Jones (Amazon, Barnes & Noble)
• A Horse Named Jim: A Clinical Trials Manual – Duke Clinical Research (Amazon, Barnes & Noble)
• The Subtle Art of Not Giving a F**K (Amazon, Barnes & Noble)

Show Notes

[0:00] Podcast Introduction & Episode Context and Objectives

• Live recording at the Research Revolution conference hosted by Florence Healthcare
• Clinical trial budgeting identified as a major study startup bottleneck
• Common challenges: slow response times, unclear justifications, misaligned expectations, and communication breakdowns

[3:09] Panel Introductions

• Brief introduction of panelists and their respective roles
• Explanation of the structure of the break out panel session

[4:11] Clinical Trial Budgeting

• Need to break from the “US” vs “Them” mentality
• Lack of responsiveness from either sponsor or site side is a major challenge in getting budgets done
  • Sometimes one group or the other is poorly resourced creating a bottleneck
• Lack of clear terminology means sometimes effort is wasted aligning on line item elements when both groups have similar expectations but use different terms

[7:03] The Importance of Budget Justification

• Justification documents help in accelerating approvals
• Groups can often review budgets before reading full contracts
• Signed, letterheaded justifications increase credibility
• Aligning fee schedules directly with budget line items
• Err on the side of overjustifying to be more expeditious and reduce time wasted on unnecessary correspondence
• Consistent process across projects helps strengthen partnerships and legitimacy as well as streamline work

[15:24] Building More Trust and Transparency into the Budgeting Process

• Give the documentation up front. Discuss any confusion or questions about it.
• Providing more detailed follow up helps to prevent letting things slip and makers remember your conversations with partners
• Justification exercises helping sites identify inefficiencies
• Discovering missed cost recovery during justification development
• Understanding what types of communication strategies different site/sponsor people respond to and what approach is convincing to them helps you to be a more effective communicator

[21:00] Early Communication Tactics that Help with Budget Negotiations

• Early Kick Off call to meet, greet and align on goals is good for expectation setting
• Detailed welcome letter providing background information on the site and who the main contacts are helps sponsors/CROs helps to kick things off efficiently
• Having a single point of contact that can help escalate/champion things at the site when others are unresponsive is very helpful

[25:06] Clinical Research Sites Balancing Flexibility and Sustainability

• You have to put your ‘trust costs’ on your budget if you want to make things sustainable
• Having internal ‘bottom line’ numbers helps in understanding how close negotiations are moving towards an unsustainable boundary 
• Sites vary in terms of their approaches so having justification for fees to Sponsors helps to make things move more smoothly
• Sustainable site operations are in the site and patient’s best interest

[30:31] Panelist Resource Recommendations

• The Subtle Art of Not Giving a F**K – not be so anxious and not over analyze decisions
• Nice Girls Don’t Get the Corner Office – practical, tactical communication, mindfulness and awareness within business
• A Horse Named Jim: A Clinical Trials Manual – Duke Clinical Research  – clinical trial operations and history

[35:10] QA Session: What are the most wasteful blocks of time in negotiations?

• Will vary significantly by therapeutic area. Vaccine vs oncology vs. imagine studies will have different requirements and hurdles
• Effort spent wasted trying to escalate things just to raise an issue to the correct person/representative
• Site selection and initiating negotiations is very important but also very time consuming 

[39:02] QA Session: How does a site move forward out of a position of being under funded?

• Bottom line budget helps to identify if you are being under funded
• Important to be fair so sites as a Sponsor if you want them to be long term partners
• Walk away from bad deals and studies that do not provide adequate financial support for your site.
• An honest and transparent phone conversation can help to realign expectations between a site and its sponsor.

[44:16] QA Session: Question 3: What changes are needed in the future to make contracting and budgets less of a bottleneck? 

• More comprehensive budgets and leveraging of past budgets in databases will help ensure fair deals and deals made in consistent structures
• Automated tools that better link the contract to the budget so changes are reflected quickly

[47:34] Closing Thank You and Episode Outro

Major Theme

1. Budget Justification as a Catalyst for Speed and Trust
   Clear, defensible, and standardized justifications reduce back-and-forth and enable faster sponsor approvals.
2. Internal Readiness and Standardization at Research Sites
   Sites that understand and document their workflows, costs, and processes are better positioned for efficient negotiations.
3. Communication, Transparency, and Escalation Pathways
   Early alignment, consistent documentation, and open dialogue between sites, CROs, and sponsors significantly reduce delays.

Selected Quotes

“You can justify what you’re requesting, because numbers and the math that you use to arrive at those numbers do not lie.”

“If you don’t understand your own workflows, how can you expect a sponsor to understand why you’re asking for what you’re asking for?”

“Transparency and consistency are the fastest ways to build trust and move budgets forward.”

Audience Question

Have you had experience working on clinical trial budget negotiations? What are some of your biggest wins or challenges? What do you hope to see change in the future?