Introduction: Parasitology is taught in Egyptian medical schools in the pre-clinical stage. Commentary stations are intensively used as a student-centered learning strategy that relies on designed questions to assimilate target knowledge through case-solving skills. Class instructor is mandatory for guiding students through different stations. Aim: The study was performed undertaken to assess students' perception of the tool. Subjects and Methods: A comparative, cross-sectional study was implemented on preclinical medical students who studied parasitology in discipline-based and integrated programs at AFCM. For data collection, a questionnaire was proposed and converted into an online survey using Google online survey Forms. Statistical analysis used: To evaluate the validity, KMO and Barlett's tests of Sphericity were used while Cronbach's alpha was used for reliability. A p-value < 0.05 was regarded as statistically significant. Results: A total of 200 students answered the questionnaire including 84 from discipline-based program (42%) and 116 from integrated program (58%).  The data collection tool demonstrated a validity of 0.778 and reliability of 0.754, with p-value < 0.001. More than 50% of the study group strongly agreed with the method to trigger knowledge assimilation while 48% endorsed it for deep learning. The facilitator role of the instructor was appreciated and not considered as a passive knowledge transmitter.  Comparing students from both programs, there was no significant difference regarding perception of the method. Notably, 6+1 students significantly preferred applying bonuses and penalties to motivate their performance compared with 5+2 candidates, (p-value 0.036). Conclusion: Commentary stations with a class instructor were found to trigger knowledge assimilation and stimulate deep learning in parasitology education for both discipline based and integrated program medical students.