It is important that universities have a scientific journal, in order to be able to disseminate the knowledge generated. The general objective was set, to analyze the scientific journals of the Peruvian national intercultural universities. The specific objectives, to determine compliance with the requirements for the indexing of scientific journals in Latindex and to propose improvements in the management of scientific journals. The Latindex methodology with 38 characteristics was used. Results, the National Intercultural University of the Central Forest Juan Santos Atahualpa has been excluded from said analysis, for not evidencing the existence of a scientific journal. It was concluded that the scientific journal of the National Intercultural University of the Amazon has fulfilled 31 characteristics, while the other two journals do not fulfill even half of the characteristics. In addition, there is an urgent need to improve the management of scientific journals, such as obtaining the ISSN, achieving indexing to improve their visibility, forming an editorial team with national and international members, and complying with the planned periodicity.