Navigating the EMA’s new fee structure: Strategies to cut costs and stay ahead

Regulation (EU) 2024/568 introduces significant updates to the European Medicines Agency’s (EMA) fee structure, impacting the budgets of pharmaceutical, biotechnology, and medical device companies. The regulation took effect on January 1, 2025, with the EMA providing subsequent Q&A clinics for human and veterinary medicine in February 2025.

These updates include increased regulatory costs, potential fee reductions for orphan drugs and products targeting unmet medical needs, and harmonization of fees.

Companies will need to submit the same number of regulatory changes but at a higher cost, adding pressure to their budgets. As a result, optimizing submission efficiency is now more critical than ever.

This article outlines the key implications for businesses and explains how companies can mitigate risks while capitalizing on new opportunities.

Increased regulatory costs - The most immediate impact of Regulation (EU) 2024/568 is the rise in fees for EMA-related regulatory activities, including:

• Market authorization applications.
• Conducting clinical trial assessments.
• Managing pharmacovigilance activities.
• Overseeing post-market surveillance.

For large pharmaceutical companies, the financial impact can be substantial. Many submit over 30,000 regulatory variations globally each year, with around 5,000 of those going to the EMA.

Assuming 2-3 Type II variations per product per year, a large pharma company with 40-50 centralized products could be submitting approximately 90 Type II variations annually.

Under the new fee structure, the cost of a Type II variation has risen from €107,300 to €163,200. This 52% increase could result in an additional €5 million in fees per year for large companies.

With regulatory budgets often flat or shrinking, absorbing these rising costs will be challenging.

To improve efficiency and remain compliant while managing expenses, companies must update their regulatory strategies and submission processes.

Potential implications for smaller enterprises - For small- and medium-sized enterprises (SMEs), the regulation presents a financial challenge due to the high upfront costs of regulatory fees, particularly for clinical trials, market authorization applications, and ongoing post-market activities.

However, under the changes, SMEs can take advantage of fee reductions and exemptions depending on the type of product, submission, and business.

Confirmed SMEs receive a discount on Type II variations, reducing costs from €163,200 to €97,920, a saving of 40% or €65,280 per submission.

Additional reductions and deferrals apply to market authorization extensions, scientific advice, periodic safety update reports (PSURs), and other submission types.

Fee reductions or exemptions are also offered for products targeting unmet medical needs, orphan drugs, and rare disease treatments.

For small businesses, these incentives provide financial relief, making continued product development more feasible despite rising costs.

Harmonization of fees across product types: A step toward transparency - A positive aspect of the new regulation is the harmonization of fees across some product types, including medical devices, medicinal products/drug products, and in vitro diagnostics.

This creates a more predictable regulatory framework, helping companies streamline product development and regulatory submission processes.

For companies operating in both pharmaceuticals and medical devices or with diverse product portfolios, this change reduces regulatory complexity and simplifies budgeting by aligning fees across product categories.

Revised regulatory timelines and impact on product launch planning - Although the regulation primarily focuses on fees, these financial changes may also affect product approval timelines.

Some companies may reprioritize regulatory submissions based on financial constraints, potentially delaying product launches. Others may seek cost efficiencies in regulatory processes to accelerate approvals while managing expenses.

For companies with ambitious launch schedules, adjusting timelines and securing sufficient resources for regulatory fees will be essential to stay on track.

Strategic financial management and risk mitigation - To navigate the increased regulatory costs, companies must implement effective financial management and risk mitigation strategies. These will be essential as businesses navigate the ever-evolving regulatory environment and attempt to reduce their financial burden.

Priorities should include:

• Regulatory incentives.
• Fee reduction incentives.
• Exploring alternative funding sources such as Government grants.
• Implementing financial risk management strategies.

Long-term strategic benefits of fee adjustments - While the initial impact of Regulation (EU) 2024/568 centers on increased costs, the long-term benefits may include:

• Greater predictability and transparency in regulatory expenses.
• Harmonized fees across product types, making financial planning easier.
• Incentives for innovation, particularly for products addressing unmet medical needs.

By aligning regulatory fees across different product categories, companies can better plan for market access, reducing uncertainty in approval costs.

Moreover, the regulation is designed to encourage investment in breakthrough therapies, ultimately driving innovation in the European pharmaceutical and medical device sectors.

How you can navigate these changes

From our experience working with clients, companies can turn these challenges into opportunities by focusing on key areas:

Regulatory budgeting and optimization:

• Understand financial commitments at every stage of product development.
• Utilize the harmonized fee structure to develop cost-efficient regulatory strategies across different product lines. These streamlined systems can minimize expenses and speed up approval times.

Strategic financial management:

• Assess your eligibility for fee reductions and explore alternative funding options.
• Leverage EU programs that support innovation in the healthcare sector to mitigate rising regulatory costs.

Product timelines & market access:

• Implement strategic launch planning to align regulatory submissions with financial resources.
• Optimize approval timelines to maximize cost efficiency.

Compliance & technology integration:

• Audit regulatory processes to ensure a seamless transition to the new framework.
• Upgrade internal systems for tracking fees and compliance management.

Summary: Prepare for change and embrace opportunity

While Regulation (EU) 2024/568 brings higher regulatory submission costs, it also presents opportunities for streamlined compliance, financial incentives, and long-term planning advantages.

To stay competitive, companies must:

• Proactively manage budgets.
• Optimize regulatory strategies.
• Explore cost-saving opportunities.

G&L Scientific has successfully helped clients navigate regulatory changes and optimize submission strategies. With expert guidance and strategic planning, companies can turn these challenges into opportunities for growth and market success.

Sarah Imrie is a Senior Regulatory Executive at G&L Scientific.