Site Payments Are Still a Mess, But Takeda Is Trying To Help

By Dan Schell, Chief Editor, Clinical Leader

There are a few constants in clinical trials.

Our trials aren’t diverse enough.

The feasibility process needs a serious upgrade.

And clinical trial sites are tired.

They are tired of waiting to get paid, tired of chasing down remittances, and tired of feeling like the one stakeholder that bears financial risk while everyone else gets to step back and talk about “innovation.” That frustration took center stage at this year’s (and I’m guessing previous years’) SCRS Global Summit in Orlando, during a lively panel on maximizing site profit margins.

One of the panelists, Heidi Barham, associate director of clinical study site payments at Takeda, has seen the problem from every angle. She spent more than a decade in site payments on the CRO side before being brought into Takeda to help internalize its site payment operations. That move alone signals a shift in how sponsors are starting to think about the burden on sites. Barham said she quickly learned how much sites wanted to be heard directly, without everything being filtered through a CRO. Historically, she said, if the sponsor and CRO were talking, “It usually meant something was wrong.” Sites picked up on that dynamic, too, and felt like they were being managed at a distance rather than supported.

Barham and her colleague now make themselves directly available to sites. She told me that even something as simple as answering an email within a day has real impact. “When sites get a response immediately and know someone is listening, it changes the tone. They don’t feel like they’re begging to be paid for work they’ve already completed,” she said.

Why Delays Happen — And Why They Hurt So Much

Slow payments aren’t just inconvenient. They can be existential.

Many independent research sites operate with only a few months of working capital. When payments take 60 or 90 days, or when sites must invoice for basic startup fees and wait again through review cycles, they are essentially financing the trial themselves. Barham noted that this is particularly damaging for smaller sites where the same staff handling patient workflows are also responsible for data entry, invoicing, and reconciliation. If data entry is delayed because that coordinator is juggling three other jobs, payments may not even be triggered. “Some sites don’t realize the payment clock doesn’t start when the visit happens. It starts when the data is complete in the EDC,” she explained.

The financial strain isn’t news. An October 2025 Pharmaceutical Executive article recently called reliable and transparent site payment operations “the new competitive advantage” — a straightforward acknowledgment that sites now have choices in which sponsors they work with, and that operational support matters as much as study design. But even knowing that, the industry has been slow to shift (I know, shocker.).

The Relationship Changes With Internal Payments

When Takeda decided to move site payments in-house, the goal wasn’t simply operational efficiency; it was relationship repair. Barham said that when sites finally had direct contact and could escalate issues immediately, the tone changed dramatically. Sites reported feeling more “visible” and more like partners rather than vendors. And because Takeda could see payment data directly, it could identify operational bottlenecks and fix them faster. One immediate process change was eliminating the requirement for sites to invoice for startup fees. Those payments are now triggered upon contract execution, which cuts out weeks of unnecessary delay.

Takeda is also rolling out a site-facing payment portal — something sites requested clearly and repeatedly. The idea is simple: Sites should be able to log in and see what payments are coming, what has already been processed, and what data is outstanding (just like you do for your online bank account). Sites shouldn’t be emailing generic addresses and hoping for a reply.

Sites Are Still Leaving Money On The Table

Profitability problems don’t come only from slow payments. They come from budgets that never covered the full scope of work to begin with. This was a big part of that SCRS session I attended.

During our interview, Barham pointed to the SCRS Site Invoice Toolkit, which lists dozens of billable items sites are often performing without reimbursement. She noted that many newer or smaller sites don’t even know the toolkit exists. “If you’re doing the work, it should be in your budget. We may negotiate the number, but the line item needs to be there,” she said.

This aligns closely with the argument made by one of my favorites in this industry, Dr. Daniel Fox of CRPN, who frequently argues that financially healthy sites are not only more sustainable but deliver better patient experiences. He encourages sites to adopt a “business unit mindset,” where every procedure, technology requirement, workflow change, and staff hour is accounted for when negotiating budgets. It isn’t opportunistic. It’s responsible site management. (Check out my article with Dr. Fox, “Being Financially Prudent As A Site Isn't a Bad Thing.”)

The sites that understand this are no longer waiting for sponsors to dictate pricing frameworks or coverage logic. They’re coming to budget discussions prepared with cost breakdowns, rationale, and evidence. They know what it costs to run a compliant, well-supported study. They know what happens if they undervalue themselves.

And they say no when they need to.

The Path Forward

Obviously, there’s no single —or quick — fix here. But I’m getting the impression that the direction is clearer than it has been in years. Sponsors paying faster and communicating directly helps. Site payment portals help. Faster data entry helps. Transparent budgeting helps. Awareness of tools and resources helps.

But the biggest shift is cultural.

Sites are no longer accepting the idea that margins just “are what they are.” They are questioning just how fair market value (FMV) is being calculated. They are beginning to act like the critical partners they are. And good sponsors — the ones thinking about long-term site partnerships and not just this quarter’s study deliverables — are responding.