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This article compares the scientific production of Peru and Ecuador between 2009 and 2018. Documents with at least one Peruvian or Ecuadorian affiliation were retrieved from the Science Citation Index Expanded, Social Sciences Citation Index, Arts & Humanities Citation Index and Emerging Sources Citation Index of the Web of Science database. The trend and exponential growth of scientific production were evaluated, more productive institutions and thematic areas were identified. The intellectual structure of the Peruvian and Ecuadorian scientific production was studied by means of the authors bibliographic-coupling analysis (ABCA) and the authors co-citation analysis (ACA). The results show that Peru has greater accumulated production than Ecuador. However, Ecuador has more production in the last three years, even with a forecast to continue producing more than Peru. The most productive institutions in both countries are the universities, and the most productive subject categories for Peru are occupational and environmental health, and for Ecuador they are educational research and environmental sciences. [ABSTRACT FROM AUTHOR]