Objectives To estimate the cost of the hospital pharmacy’s participation in clinical trials (CTs) and to compare it to the amount received in compensation from sponsors.

To analyse the financial impact of CTs that end without recruiting any patients and without any financial compensation from promoters.

Methods This retrospective observational study analysed data from 5 years (2014–2018) at a tertiary university hospital.

We established an allocation formula taking into account direct costs related to the pharmacy department’s CT area’s activity (reception, safekeeping, preparation, devolution, and destruction of medication, as well as patient monitoring) and indirect costs (facilities, resources, support staff). We calculated the costs to the department and the compensation received both overall and based on the type of promoter, clinical department involved in the trial, and the number of patients included.

Results We included 134 trials. Costs added up to €207 372.95 and the compensation to €149 128.93 (€58 244.02 loss for the department). Trials ending without recruiting patients (33.6%) and without compensation accounted for 57.45% of the deficit. The mean cost of trials ending without recruiting patients was €875. We plan to charge a reimbursable setup fee for opening CTs to safeguard against these losses (€875 for trials in all departments except oncology; €1100 for oncology because 38% of their trials end without recruiting patients) and to compensate for the costs incurred in participating in trials for cooperative groups without financial compensation (20%).

Conclusions Billing sponsors based on costs incurred for each trial would be a fairer system than the current approach based on the number of patients included. Establishing an initial fee would make up for losses from trials that fail to recruit any patients.