When the social distancing guidelines, as a result of the COVID-19 pandemic, caused universities to close campuses, there was a rapid shift in the course delivery methods of human gross anatomy laboratory sessions. Courses were delivered online, and this change created new challenges for anatomy faculty to engage students effectively. This profoundly impacted student-instructor interactions, the quality of the learning environment, and successful student outcomes. Because of the importance of student interaction and engagement for hands-on laboratory courses like anatomy, which rely on cadaver dissections and in-person learning communities, as well as the novel opportunity, this qualitative study sought to explore the faculty perspectives of transitioning their in-person laboratory sessions online and unearth their experience with student engagement in this new teaching format. The Delphi technique was used to explore this experience in two rounds of qualitative inquiry using questionnaires and semi-structured interviews, and thematic analysis was used to analyze the data, identifying codes and building themes. The study utilized indicators of student engagement in online courses to formulate four themes: instructor presence, social presence, cognitive presence, and reliable technology design and access. These were constructed based on the factors faculty used to maintain engagement, new challenges they faced, and strategies deployed to overcome these challenges and engage students in the new learning format. These are supported by strategies such as using video and multimedia, ice-breaker activities, chat and discussion features, immediate and personalized feedback, and virtual meeting via synchronous sessions. These themes highlight important lessons that faculty designing online anatomy laboratory courses can use to guide their course design, and institutions and instructional design faculty can use to inform best practices and faculty development efforts. Additionally, the study calls for further research to design a standardized and global assessment tool that measures student engagement in the online learning environment.