Introduction: Many teaching institutes adopted the online teaching system during COVID-19 pandemic. The Department of Anatomy Armed Forces Medical College had also shifted to online platform for teaching anatomy in a better way.This study was undertaking with an aim to get the student`s perspective about the efficacy of online teaching system for learning anatomy and to explore and rectify the lacunae and address the challenges faced by students and teachers. Methodology: a total of 300 students were enrolled, 150 each from 1st year MBBS of batches 2019 and 2020 Results: Findings suggested that student's perception towards online learning was better than offline learning. However, the major challenges were problems in internet connection, practical anatomy, having to learn more points related to the topic in a short allocated time and difficulties in logging onto the online platforms.The reliability of internet connection was a major factor affecting their study of anatomy and selecting learning resources.Social media platforms especially WhatsApp were helpful in assisting students in their study and communication between themselves and their teachers, may be because of lesser use of bandwidth. However, assessments and practical demonstrations in anatomy were not same as during offline teaching mode.Conclusion: COVID-19 pandemic was disruptive to medical education. Poor Internet connection was the major bug bear faced by the students, while the social media platforms especially WhatsApp was a helpful tool in study and communication. Students urged improvement in the modes of practical teaching of anatomy and assessment.