Recent advance in medical education is in correlation with the advances in information technology and thus computer-based learning is being increasingly employed. The objective of the present study was to design and evaluate an e-learning module in anatomy and assess the perceptions of students and faculty about this e-learning module. The participating students were randomized into three groups by block stratified randomization and Google groups were created for each of the three groups. The e-learning module was implemented in three sessions by rotating the three groups. Validated questionnaires were sent to faculty and participating students via Google forms to obtain feedback. The results of ANOVA showed that there was a significant difference among the groups in terms of marks obtained with conventional (F = 2.403, P = 0.103), online (F = 6.050, P = 0.005), and blended (F = 5.801, P = 0.006). Post hoc comparisons using the Tukey HSD test, about the gain of knowledge, indicated that the results were insignificant when comparing the conventional group with the online group, but were significant when comparing the blended group with the conventional and online group. The qualitative data regarding the perception of students toward e-learning were analyzed using thematic analysis. The introduction of an interactive e-learning module in anatomy was effective and well received by the students and faculty. The study showed that blended learning has a positive impact on the students' learning by improving cognitive gain and receptive perception for e-learning.