Introduction: Mental health is a priority public health problem, with medical students being a group susceptible of suffering from mental disorders. Objective: To determine the association between, on the one hand, the presence of depression, stress and/or suicidal ideation and, on the other, the academic performance of medical students from a Peruvian university in the midst of the COVID-19 pandemic. Materials and methods: Cross-sectional, analytical and prospective study carried out in 241 students from 1st to 6th year of medicine. Data collection was carried out between March and May 2021. The presence and levels of stress, depression and risk of suicidal ideation were determined using the Perceived Stress Scale-14 (EEP-14), the Zung Scale for Depression (EZ-D) and the Beck Suicidal Ideation Scale (ISB), respectively; on the other hand, academic performance was evaluated with the Reyes Murillo learning assessment scale. A bivariate analysis was performed using the chi square test (significance level of p<0.05) to establish the association between the study variables. Results: Most of the students had an average academic performance (70.12%). The prevalence of depression, stress, and suicidal ideation was 33.61%, 94.19%, and 88.79%, respectively. Academic performance was significantly associated with the presence of depression (p=0.018), but not with the presence of stress (p=0.669), or risk of suicidal ideation (p=0.438). Conclusions: Only depression was significantly associated with academic performance, although its prevalence was much lower than stress or suicidal ideation, so it is necessary for the university to implement strategies aimed at improving the mental health of this population; this will not only improve its quality of life, but also its academic performance.