How Technology is Transforming Drug Rebate Management

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Medicaid’s launched its multiple best price program in July 2022 to address a major regulatory barrier to value-based drug pricing arrangements. Policy makers hope with this potential contracting risk and liability gone, manufacturers and healthcare payers will increase their participation in value-based drug pricing agreements.
In 1990, the Medicaid Prescription Drug Rebate Program (MDRP) was created to help slow the expenditures of outpatient prescription drugs to Medicaid patients. Under the MDRP, drug manufacturers who want their drugs covered by state-run Medicaid programs must sign a National Drug Rebate Agreement (NDRA) with the Department of Health and Human Services (HHS).
The NDRA requires participating manufacturers to reveal the lowest available price of their products and pay rebates on their products. According to the Centers for Medicare and Medicaid (CMS), there are around 780 drug manufacturers with NDRAs currently in effect.
The rebates of the Medicaid Best Price Policy
Under the MDRP, manufacturers must inform CMS of the “best price” available for its products. Excluding the price negotiated with some government programs, manufacturers are required to report the lowest price it offers to any drug wholesaler, retail outlet, or healthcare provider. This best price is then used to calculate rebates. Manufacturers pay rebates quarterly to states for the drugs covered under state Medicaid programs.
The rebate for most brand name drugs (excluding certain clotting drugs and pediatric drugs) is 23.1% of the average manufacturer price (AMP) paid by wholesalers and retail pharmacies. If the difference between the AMP and the best price on the market is more than the AMP, then this percentage would become the rebate. The rebate amount for generic drugs does not include a best price provision and stands at 13%.
Rebate analysis plays a critical role in understanding these calculations, as it enables manufacturers and payers to evaluate the financial implications of pricing agreements and compliance with regulatory requirements under the MDRP.
Outcome-based drug pricing can affect rebates
Despite the industry-wide push from stakeholders and policy makers towards value-based drug pricing arrangements, manufacturers have been wary of signing on to these agreements. They argue these outcomes-based pricing agreements could have unintended consequences that affect the AMP and best price. This, in turn, can skew the calculations for a manufacturer’s rebate liability.
In value-based drug pricing, a drug’s purchase price is linked to the effectiveness of the drug; if the drug underperforms, the manufacturer must pay a rebate, or other form of reimbursement, to the purchaser. Depending on the terms of the value-based pricing arrangement, this could be a substantial reimbursement to a payer for poor patient outcomes. The reduced price after the rebate–even if it’s paid on behalf of only one patient’s poor outcome–could become the new, lower best price.
The new Multiple Best Price policy
Before the multiple best price policy went into effect, manufacturers feared that, in theory, if the terms of a pricing agreement resulted in a 100% reimbursement to a payer for a drug proven to be ineffective, the manufacturer could find themselves in a situation where they had to give away their drug for free to every state Medicaid program.
In response to this interpretation of the best price policy–which became a regulatory barrier to value-based drug pricing arrangements–CMS revised the best price policy with the Final Rule. Under the Final Rule, as of July 2022, manufacturers can now report multiple best prices: the single best price for traditional sales and the prices negotiated under value-based pricing arrangements.
This option to report multiple best prices to CMS is only available for manufacturers who offer states the same terms negotiated in the value-based drug pricing arrangements with commercial insurances. State Medicaid programs can choose to take part in the value-based arrangements or continue to make purchases using the traditional best price.
Critique of the Multiple Best Price policy
Although CMS’ goal with the multiple best price policy was to reduce a significant regulatory barrier, this change still draws critics. And CMS has acknowledged that there will be implementation challenges. Here are some examples of criticisms of the new multiple best price policy.
• Critics find the Final Rule’s updated definition of a value-based drug pricing agreement to be too narrow or too broad. Before the Final Rule went into effect, organizations such as the Coalition for Affordable Prescription Drugs (CAPD) and the Pharmaceutical Research and Manufacturers of America (PhRMA) were concerned the CMS definition of value-based contracting is too narrow and will exclude some value-based pricing arrangements that are already in effect or in negotiations.
By contrast, AARP worried there is a lack of clarity on the definition of value in the Final Rule that could lead to the designation of almost any drug purchasing agreement as a value-based agreement and open the door to fewer rebates for Medicaid programs and more revenue for manufacturers. Time will tell which is the real problem.
• There may not be a non-value-based price for a drug. If a manufacturer is not offering its product outside of a value-based pricing arrangement, there may not be a single, traditional best price to report. When there are no non-value-based sales to look at, CMS advises manufacturers to use reasonable assumptions to set a non-value-based price. Critics, of course, question the loose guidance of a “reasonable assumption” and see this as an opportunity for manufacturers to game the system.
Some stakeholders are also concerned manufacturers will shift most traditional sales contracts to value-based pricing arrangements with the goal of eliminating less profitable, non-value-based best prices. AARP and National Association of Medicaid Directors (NAMD) have warned that the new rule could undermine the MDRP best price policy that has been so successful in reducing Medicaid drug expenditures.
• There may be technological and operational barriers for State Medicaid programs who want to take part in value-based drug pricing agreements. Like NAMD and AARP, the National Organization for Rare Disorders (NORD) worries manufacturers could be working to erode the MDRP’s best price policy by providing better rebates to commercial insurance companies under value-based pricing arrangements.
Manufacturers and CMS know that some state Medicaid programs will not have the infrastructure needed to implement value-based pricing agreements with more favorable terms. In its Technical Guidance for using multiple best prices, CMS makes suggestions for creating alternative, innovative agreements when intensive data collection and analysis are not feasible.
Related Post: Indication-specific pricing to make inroads in the U.S.
The Lyfegen Solution
A lack of resources and staff prevents some state Medicaid programs from operationalizing value-based drug pricing arrangements. Lyfgen assesses an organization’s current data gathering capacity, then offers customized solutions using its contracting software platform to support the execution of value-based drug pricing arrangements.
Lyfegen’s Platform helps healthcare insurances, pharma, and medtech companies implement and scale value-based drug pricing contracts with greater efficiency and transparency. By collecting real-world data and using intelligent algorithms, the Lyfegen solution can provide valuable insights into drug performance and cost in value-based contracts.
Lyfegen helps increase affordability and access to healthcare treatments by enabling the shift away from volume-based and fee-for-service healthcare to value-based healthcare.
Contact us to learn more about Lyfegen’s software solutions and to book a demo.
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The complexity of drug rebate management has grown significantly in recent years. With multiple rebate structures, evolving regulations, and limited visibility across the process, pharmaceutical companies and payers face increasing challenges in tracking, optimizing, and ensuring compliance in rebate agreements.
Traditional rebate management often relies on manual processes, spreadsheets, and siloed data sources—leading to inefficiencies, errors, and revenue leakage. But technology is changing that. Automation, real-time analytics, and centralized platforms are transforming how pharma and payers approach rebate strategies.
Automation and AI
Advanced Analytics and Predictive Modeling
Improved Compliance & Transparency
The future of rebate management isn’t manual—it’s intelligent, automated, and built for scale. That’s exactly where Lyfegen comes in.
Our Rebate Analytics Platform is designed to help both payers and pharmaceutical companies take control of growing complexity. With automation, analytics, and real-time insights at its core, Lyfegen enables your team to:
Payers and pharma leaders around the world are already using Lyfegen to recover lost revenue and gain full visibility into their rebate performance.
Now it’s your turn. 👉 Book a demo and see how Lyfegen transforms rebate management—starting today.
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With price tags in the millions, gene therapies are redefining medicine—and reshaping how we negotiate access to it. For both payers and pharmaceutical companies, these breakthrough treatments present a shared challenge: how do you fund what feels priceless?
From Zolgensma to Hemgenix, gene therapies promise one-time cures for rare and life-threatening diseases. But the financial model behind them can’t follow the traditional playbook. These treatments call for a smarter, more collaborative approach to pricing—and that’s exactly what’s taking root.
Why Payers and Pharma Need a New Playbook
Unlike conventional drugs, gene therapies frontload their cost while delivering benefits over time. That disconnect forces a fundamental rethink of how pricing, reimbursement, and risk-sharing are handled.
According to the Lyfegen 2024 Drug Contracting Trends Report, health systems worldwide are moving toward innovative agreements: outcome guarantees, installment plans, and subscription-based models. These aren’t just experiments—they’re becoming essential tools to balance patient access with financial responsibility.
For payers, it’s about managing risk while maintaining equity. For pharma, it’s about demonstrating value in a way that aligns with clinical reality. Either way, the direction is clear: shared risk, shared benefit.
Global Shifts That Are Shaping the Market
The trends are global and accelerating. In the United States, payers like Blue Cross Blue Shield and Medicaid are embracing outcome-based models for sickle cell gene therapies like Casgevy and Lyfgenia. Brazil’s Ministry of Health uses installment payments for Zolgensma, spreading risk over five years while tying reimbursement to real-world outcomes.
In Europe, countries like Spain and Italy combine restricted coverage with annual reassessments, ensuring that high-cost therapies are only reimbursed if they continue to deliver results.
The message? Pricing innovation is no longer a nice-to-have—it’s the only way forward.
How Lyfegen Bridges the Gap
At Lyfegen, we help payers and pharma move beyond the negotiation table—and into action.
• Our Agreements Library, the world’s largest digital repository of value-based contracts, helps you understand what others are doing and where the benchmarks lie.
• Our pricing simulation engine lets both sides explore scenarios before committing—making deals smarter from day one.
• And our automated platform handles everything from contract setup to rebate tracking, saving time, reducing risk, and driving transparency.
A Smarter Way to Fund the Future of Medicine
Gene therapies will continue to challenge the limits of what we think healthcare can afford. But with the right models and tools, both payers and pharma can find common ground—ensuring that innovation reaches the patients who need it most.
Curious about what’s next in drug contracting?
Download the 2024 Drug Contracting Trends Report for exclusive insights, real-world examples, and global benchmarks.