Background: Simulation-based training allows trainees to experiment during training and end-of-training tests could increase motivation and retention. The aim of this trial was to determine if a simulation-based training program including directed self-regulated learning and post-testing improved clinical outcomes compared to a traditional simulation-based training program. Methods: A randomized trial was conducted involving 32 participants without prior experience in endoscopic procedures. The intervention group practiced independently in a simulation centre and got a post-test whereas the control group received traditional instructions and demonstrations before being allowed to practice. Three weeks after the intervention the participants performed cystoscopies on two consecutive patients. Clinical performance was assessed using a global rating scale (GRS) with established evidence of validity. Independent samples t-test, Cronbach's α, Pearson's r, and paired samples t-test were used for statistical analysis. Results: Twenty-five participants performed two cystoscopies on patients. There was no significant difference between the two study groups with respect to mean GRS of performance (p = 0.63, 95 % CI; -2.4–3.9). The internal consistency of the global rating scale was high, Cronbach's α = 0.91. Participants from both study groups demonstrated significant improvement between the first and second clinical procedures (p = 0.004, 95 % CI, 0.8–3.5). Eight (32%) and 15 (60%) participants demonstrated adequate clinical skills in their first and second procedure, respectively. Conclusions: No significant differences were found on the clinical transfer when comparing the two programs. Neither of our training programs was able to ensure consistent, competent performance on patients and this finding could serve as an important argument for simulation-based mastery learning where all training continues until a pre-defined level of proficiency is met. Trial registrations: The trial was submitted before enrolment of participants to the Regional Scientific Ethics Committee of the Capital Region which established that ethical approval was not necessary (H-4-2014-122). The trial was registered at Clinicaltrials.gov (NCT02411747). Health profession; Medicine; Education; Directed self-regulated learning; Mastery learning; Transfer; Testing effect; Flexible cystoscopy; Virtual reality simulators