Unifying Study Finance Operations for Life Sciences | Real-Time Budget Tracking & Audit-Ready Accuracy

The Challenge

A global biopharmaceutical company running several large-scale clinical trials across therapeutic areas needed a better way to manage study-level financials.
Each trial had different contracts, vendor payment terms, site reimbursements, and patient-related costs. The financial data came from multiple systems, Clinical Trial Management System (CTMS), Electronic Data Capture (EDC), and enterprise ERP, all using different data structures and timelines.

Key challenges included:

Disjointed Financial Ecosystem
Budgets were approved centrally but tracked separately by regional affiliates and CRO partners. This created misalignment between planned vs. actual spend for site payments, investigator fees, and vendor invoices.
Site Payment Complexity
Study sites invoiced based on visit milestones, patient completions, or procedure frequency. Payments were processed manually and often validated against spreadsheets, increasing turnaround time and missing visibility on pending reimbursements.
Vendor and System Fragmentation
Vendors providing lab services, logistics, or technology (EDC, IRT, eTMF) submitted invoices in different formats and currencies. The reconciliation of these with internal ledgers required multiple validation steps and manual corrections.
Budget Forecasting Gaps
Finance teams found it difficult to compare forecasted budgets against actual spend in real time. Without a unified financial view, identifying overspend trends or under-utilized budgets across trials was delayed.
Audit and Compliance VisibilityEvery clinical study required traceable documentation of financial transactions for audit and inspection readiness. Since data existed across several platforms, building a single audit trail for payments and vendor spend consumed time and resources.

Our Solution

Agilisium developed a Clinical Trial Finance Reconciliation and Budget Transparency Framework, integrating financial data across study systems and enterprise tools to provide unified visibility, automated validation, and continuous audit readiness.

Integrated Financial Data Model

The framework connected key data sources, CTMS for study and site milestones, EDC for patient visit activity, and ERP for invoices and payments. This created a single reconciled dataset that linked each payment to a clinical event or budget category.

Automated Invoice Matching and Validation

The system applied predefined logic to compare vendor and site invoices with study budgets, POs, and visit data. Rules identified duplicate records, incorrect visit claims, and unmatched currency or tax values. Approved invoices were automatically validated and routed for payment.

Budget Utilization Insights

Dynamic dashboards allowed finance and study teams to view budget burn rates, committed spend, and variance against forecast. Users could drill down by protocol, country, or vendor type to assess where budget adjustments were needed.

Continuous Audit Trail

Each reconciliation step, approval, and exception was captured automatically. The resulting audit-ready trail allowed finance and compliance teams to trace every transaction back to its originating study and supporting document.

Collaborative Workflow Between Finance and Clinical Operations

Role-based access ensured that finance controllers, study managers, and vendor leads worked from the same dataset. This reduced version conflicts and ensured consistency across regions and CRO partners.

Key Impact

85%

Reduction in manual reconciliation effort for site and vendor payments

Real-time visibility into study-level and portfolio-level spend

The Customer

A global biopharmaceutical enterprise conducting multi-country Phase II–IV clinical trials across oncology, immunology, and rare disease programs.

The Outcomes

Unified Financial Oversight Across Studies

Study and vendor payments are now reconciled automatically against trial budgets and patient visit data, providing one consistent view across all ongoing programs.