Background: Human Anatomy is a challenging subject in the MBBS curriculum due to its complex 3D structures and its foundational role in understanding other medical subjects. Conventional teaching methods, including lectures, dissections, and demonstrations, often fail to provide the required 3D visualization. With the advent of technology, virtual learning tools have emerged as potential aids, offering interactive and accessible learning experiences. However, their effectiveness compared to traditional methods and their impact on students' perception and learning outcomes need to be evaluated. Method: This study was conducted in the Department of Anatomy, MGM Medical College, Indore, to assess the perception of virtual learning tools among 1st-year medical students. A total of 240 students aged 17-23 years, who participated in both traditional classroom-based anatomy education and utilized various e-learning tools, were included. Data was collected using a Google Form questionnaire covering demographic details, resources used (e.g., educational videos, eBooks, interactive apps), and devices used for learning. The study aimed to understand the effectiveness of these tools and whether they can supplement or replace conventional teaching methods. Results: The study revealed that 57.1% of the participants were males and 42.9% were females. 81.25% of students had an urban schooling background, while 18.75% were from rural areas. Educational videos were the most popular learning resource (95.8%), followed by eBooks and eJournals (53.0%) and interactive anatomy apps (42.1%). Mobile phones were the most commonly used device (92.1%), followed by iPads/Tablets (34.4%). The study highlighted that virtual tools enhance interactive and independent learning but also have negative aspects, such as increased screen time leading to neck pain, eye strain, and headaches. Conclusion: The study provided valuable insights into students' perception of virtual learning tools for anatomy education. While these tools promote interactive and supported learning, they cannot completely replace the traditional role of teachers in mentoring, guiding, and evaluating students. Instead, they can be incorporated as part of a blended learning approach. As virtual learning tools become increasingly popular, there is a need to optimize educational design and technology to maximize learning opportunities. Understanding students' perceptions is crucial to effectively integrating these tools and enhancing learning outcomes.