The study investigated how utilizing a 3D virtual application relates to academic performance in Peruvian medical students, while also exploring additional factors that could impact their academic outcomes.” We carried out a cross-sectional analytical study involving students enrolled in the Musculoskeletal System course in the first semester of 2019. Participants provided information through a structured data form and completed the adapted Self-Directed Learning Readiness Scale (SDLRS) by Fisher, King, and Tangle. To explore the link between effective use of the 3D application and academic performance, linear regression analyses were conducted. Additional factors influencing academic performance were examined using nested models, with β coefficients estimated via manual forward selection. The study included 187 medical students, 61% of whom were female, with a median age of 21 years (range 20–22). The average grade was 13.5 ± 2, and only 21% reported consistently using a 3D application. After adjusting for covariates, there was no significant link between 3D app usage and academic performance (aβ = 0.17; 95% CI: -0.45 to 0.80). Academic performance was negatively associated with age (aβ = -0.22; 95% CI: -0.39 to -0.06) and prior failure in anatomy or physiology courses (aβ = -2.11; 95% CI: -2.9 to -1.8), while engagement in extracurricular activities showed a positive association (aβ = 0.75; 95% CI: 0.25 to 1.24).” Proper utilization of a 3D application for learning musculoskeletal anatomy did not show a significant impact on students’ academic performance.