Understanding the fundamental role anatomy education plays in medical training and taking into consideration the nascence of online education in Nigeria, this study evaluated the perceptions of medical and allied-health students toward online anatomy education both during the COVID-19 lockdown in Nigeria and for the future. For this study, Google Form questionnaires were distributed via different social and academic platforms to medical and allied-health students in Nigeria between September 28 and December 17, 2020. A total of 954 students participated in the study and 947 valid responses were recorded. The results showed that 77.6% of the students had reported computer/IT skills and 12.1% admitted that they had never attended an online class. Interestingly, 60% of the respondents disapproved of online learning approaches as effective tools for instructions in the anatomical sciences. Majority of the students (84%) agreed that their performance in anatomy would have been better if the classes were face-to-face, while 55% found the online anatomy classes uninteresting. Furthermore, 91.5% agreed that anatomy educators needed advanced skills for online education, while 94.2% agreed that anatomy online teaching needs more advanced technology to be implemented in Nigeria. This study revealed an overall negative perception about the suitability and effectiveness of online anatomy education in Nigerian medical/health training. This study recommends further investigations into the challenges that were presented during online anatomy education at the peak of the pandemic. This will help direct the development and implementation of a workable and sustainable online education model for anatomical sciences in Nigeria.