Purpose: Studies objectively comparing lithotomy and prone positions regarding surgeon comfort, ergonomics, patient comfort, and position related complications are scarce. Methods: The patients posted for surgery of either fistula in ano, hemorrhoids, or were included in this study. Subjective Mental Effort Questionnaire (SMEQ) and Local Experienced Discomfort (LED) scale were used to score the level of mental and physical stress among the operating surgeon, assistants, and the scrub nurse. Other parameters studied were the exposure of the operative site, patient comfort level, and position-related complications. Results: Thirty patients were operated in each position. Mean±standard deviation of jackknife prone vs. lithotomy surgeon SMEQ score (15.6±10.4 vs. 107.0±11.5, P<0.05) and LED score (1.8±1.5 vs. 6.7±0.5, P<0.05) were found to be statistically significant. Prone vs. lithotomy assistant SMEQ score (29.1±13.1 vs. 100.6±8.7, P<0.05) and LED score (4.6±1.1 vs. 7.4±0.8, P<0.05) were also found to be statistically significant. SMEQ (10.0±0.0 vs. 20.6±2.5, P<0.05) and LED scores (1.1±0.3 vs. 3.3±0.5, P<0.05) of scrub nurses and LED scores (2.5±0.5 vs. 6.3±0.7, P<0.05) of patients were also statistically significant. Exposure of the operative site was significantly better in the prone position (5.0 vs. 2.1, P<0.05). Conclusion Significantly better SMEQ, LED, and exposure score suggests the superiority of jackknife prone position over the lithotomy in terms of significantly less mental and physical stress to the operating surgeon, assistant, and scrub nurse; better ergonomics, and excellent exposure.