Studies of research policies and scientific production are essential for strengthening educational systems and achieving objectives such as quality improvement. The aim of this study was to evaluate the influence of research policies on the scientific production of public and private Peruvian universities. An observational, descriptive, secondary analysis study of the research policies of 92 universities and two graduate schools licensed by the National Superintendence of Higher Education of Peru (SUNEDU) was conducted for the period from 2016–2020. Scientific publications from educational institutions were collected from Scopus and Web of Science for the study period, and researchers certified by the National Council of Science and Technology of Peru (CONCYTEC) were divided by group and level. Multiple regression analysis was performed using two models. The analysis indicated that research policies did not influence scientific production in Scopus or Web of Science in either 2019 or 2020 (Model I) but that type of management (p < 0.01), number of National Scientific, Technological, and Technological Innovation Registry (RENACYT) researchers (p < 0.001) and 2016 scientific production (p < 0.001) did influence production when these variables were incorporated into the model (Model II). However, time of licensing and management type had no effects. The number of research policies implemented by Peruvian universities and licensed graduate schools was not large. Therefore, it is recommended that project funding policies, research training, and research collaboration be strengthened and that the management capacity of research centers and institutes be increased.