Objective To determine the presence of a gender gap in the scientific production among Peruvian physicians and analyze either gap is associated with the presence of observable factors or the presence of prejudices against female physicians. Methods We analyzed data from the National Survey of User Satisfaction in Health 2016, a nationally representative survey that collected information about medical professionals working in health institutions in Peru. The outcome of interest was the number of publications in indexed journals. We estimated the gender gap in scientific production using the Oaxaca-Blinder (OB) decomposition method. Results From the 2216 physicians surveyed, 252 reported published at least one article in an indexed journal. From physicians with scientific production, 37.7% were women. The analysis of OB decomposition showed a gap of 2.11 indexed publications, disfavoring female physicians (p<0.01). Likewise, the explained component was 1.36 publications, representing 64.5% of the total gap (p<0.05). Conclusions There is a gender gap in the number of publications in indexed journals among Peruvian physicians. This gap is mainly explained by observable factors, such as the years of medical practice, being an accredited researcher and being a professor.