Background: Mastering laparoscopy is challenging—it requires specific psychomotor skills which are difficult to obtain in the operating room without potentially compromising patient safety. Proficiency-based training programs using virtual reality simulators allow novices to practice and develop their skills in a patient-safe learning environment. Variable practice leads to stronger retention and skills transfer in a non-surgical setting. The objective of this trial was to investigate if variable practice was superior to self-directed training. Methods: A randomized trial where participants (n = 36) were randomized to proficiency-based laparoscopic simulator training of basic skills using either variable practice or self-directed training, followed by a transfer test with proficiency-based training on a procedural task (a salpingectomy). All participants returned after a period of 3–5 weeks to perform a retention test. Results: The mean time to proficiency for the basic skills tasks were 119 min (SD: 93) for the variable practice group versus 182 min (SD: 46) for the self-directed training group (p = 0.015). The time to reach proficiency during the transfer test was 103 min (SD: 57) versus 183 min (SD: 64) for the variable practice group versus the self-directed training group, respectively (p < 0.001). The mean time to proficiency for the retention test was 51 min (SD: 26) and 109 min (SD: 53) for the variable practice group and self-directed training group, respectively (p < 0.001). Conclusion: Variable practice is superior to self-directed training for proficiency-based laparoscopic training. With variable time to practice proficiency is reduced, there is higher transfer to a procedural task, and retention is improved.