In response to the COVID-19 pandemic, medical educators have transformed pre-clerkship anatomy curricula into online formats. The purpose of this study was to evaluate the effectiveness and student perceptions of an online near-peer anatomy curriculum. The classes of 2022 and 2023 completed identical foundational anatomy curricula in-person, whereas the class of 2024 completed an adapted curriculum for remote online learning. Quantitative and qualitative responses were used to compare attitudes between instructional methods. Assessment scores and evaluation survey responses were collected from the classes of 2022 (n = 185), 2023 (n = 184), and 2024 (n = 183). Mean assessment scores (±SD) for the classes of 2022, 2023, and 2024 were 93.64% (±5.86), 93.75% (±4.09), and 92.04% (±4.83), respectively. Post hoc group comparisons showed the class of 2024 scored significantly lower than the two previous classes [2022: (H(1) = 18.58, P < 0.001), 2023: (H(1) = 18.65, P < 0.001)]. Mean survey results concerning curriculum quality were 4.06/5.00 for the class of 2023 and 3.57/5.0 for the class of 2024 (t(365) = 2.67, P = 0.008). Considering a small effect size (?[superscript 2] = 0.034), there was no meaningful difference in student assessment scores. A potential drawback of online near-peer anatomy teaching remains in student perceptions of course quality; qualitative feedback suggested technological limitations and perceptions of online course instructors were partly responsible for lower student satisfaction. Following the COVID-19 pandemic, medical educators should incorporate the lessons learned from this unique educational inflection point to improve curricula moving forward.