Objective: To evaluate the factors associated with the intention to participate in COVID-19 vaccine clinical trials in the Peruvian population. Methods: Cross-sectional study and secondary analysis of a database that involved Peruvian population during September 2020. The Poisson regression model was used to estimate the associated factors. Results: Data from 3231 individuals were analyzed, 44.1% of whom intended to participate in COVID-19 vaccine clinical trials. Factors associated with the outcome were being male (RPa: 1.25; 95% CI: 1.15–1.35), being from the highlands region (RPa: 1.18; 95% CI: 1.09–1.28) or jungle (RPa: 1.30; 95% CI: 1.15–1.47), having a relative that is a healthcare professional (PRa: 1.16; 95% CI: 1.06–1.28), using a medical source of information (PRa: 1.28; 95% CI: 1.17–1.41), and trusting in the possible effectiveness of vaccines (PRa: 1.40; 95% CI: 1.29–1.51). The main reason for not participating in the trial was the possibility of developing side effects (69.80%). Conclusion: There is an urgent need to generate a perception of safety in COVID-19 vaccine clinical trials, to increase the population's intention to participate in these studies, and to provide evidence-based information about the vaccine.