Medication reconciliation (MedRec) in hospitals is an important tool to enhance the continuity of care, but completing MedRec is challenging. The aim of this study was to investigate whether queueing theory could be used to compare various interventions to optimise the MedRec process to ultimately reduce the number of patients discharged prior to MedRec being completed. Queueing theory, the mathematical study of waiting lines or queues, has not been previously applied in hospital pharmacies but enables comparisons without interfering with the baseline workflow. Possible interventions to enhance the MedRec process (replacing in-person conversations with telephone conversations, reallocating pharmacy technicians (PTs) or adjusting their working schedule) were compared in a computer experiment. The primary outcome was the percentage of patients with an incomplete discharge MedRec. Due to the COVID-19 pandemic, it was possible to add a real-life post hoc intervention (PTs starting their shift later) to the theoretical interventions. Descriptive analysis was performed. The queueing model showed that the number of patients with an incomplete discharge MedRec decreased from 37.2% in the original scenario to approximately 16% when the PTs started their shift 2h earlier and 1 PT was reassigned to prepare the discharge MedRec. The number increased with the real-life post hoc intervention (PTs starting later), which matches a decrease in the computer experiment when started earlier. Using queueing theory in a computer experiment could identify the most promising theoretical intervention to decrease the percentage of patients discharged prior to MedRec being completed.