Introduction Medical schools face shortage of cadavers for teaching anatomy, more pronounced with COVID-19 pandemic and decrease in procurement of cadavers. Students over the years are getting averse to the cadaver due to awareness of dangers related to components of the embalming fluid like formaldehyde and complain of dissection as a stressful instruction. Aim To introduce and evaluate feasibility, acceptability and effectiveness of Computer Based Simulation (CBS) for teaching Anatomy to undergraduate students. Objectives To introduce Computer-based simulation for teaching human anatomy to medical undergraduates. To assess the feasibility and acceptability of Computer-based Simulation (CBS) teaching for human anatomy for medical undergraduates. To evaluate the effectiveness in learning human anatomy by online Computer Based Simulation teaching Methodology After obtaining ethics approval, this prospective crossover randomized controlled study was conducted online on two modules in the head and neck region by teaching on pre-prepared Videos by both cadaveric and computer simulation techniques. Pre and post test and anonymous feedback were taken Teachers’ perceptions of the students’ understanding of anatomy and the teaching methodology were assessed by written feedback forms. Results Significant difference was observed in mean score of both the techniques (p=0.033). The mean score of students taught via CBS was significantly higher than the cadaveric group. An overwhelming 88% of participants agreed that teaching via the CBS would be safer in the pandemic. Faculty was satisfied by CBS teaching as almost 90% of them appreciated the quality of student interaction and experience of teaching via CBS. Conclusions The study concludes that it is feasible to use computer-based simulation technique for teaching anatomy to Phase I MBBS students. The feedback given by the students showed that the CBS teaching method was acceptable to them as it gave them a good insight into 3- D understanding of the human body increased their understanding of the relations of body structures and organs and increased their capacity to grasp surface anatomy. It was an effective method of learning by the students and was found to induce a significant improvement in their understanding and perception. Teaching faculty also accepted computer-based simulation technique as an effective method of teaching.