The discipline of anatomy is one of the pillars of training in higher education courses in health area. Since its origin, this discipline has used the traditional method as an educational strategy. Since then, the discipline has undergone changes, including other teaching methods, such as active methodologies. With the COVID-19 pandemic, declared in March 2020 and the closure of higher education institutions, the teaching of anatomy was impacted, since it was necessary to adapt the modality of face-to-face teaching to remote teaching. The present study aims to evaluate the perception of teachers regarding students’ anatomy learning in relation to the types of methodologies applied in remote teaching during the pandemic. For such, a cross-sectional study was carried out, which analyzed the answers of 101 anatomy teachers. The results showed that there was no statistically significant difference regarding teachers’ perception of learning in relation to the type of methodology used in remote teaching during the pandemic. There was also no difference in comparing perceptions regarding the type of methodology used before and during the pandemic. Given this, these data encourage the need for reflection in the academic community and new studies with educators and students, in order to identify factors that may improve the quality of anatomy learning.