Bibliometric analysis is a commonly used tool to assess scientific collaborations within the researchers, community, institution, regions and countries. The analysis of publication records can provide a wealth of information about scientific collaboration, including the number of publications, the impact of the publications, and the areas of research where collaborations are most common. By providing detailed information on the patterns and trends in scientific collaboration, these tools can help to inform policy decisions and promote the development of effective strategies to support and enhance scientific collaborations between countries. This study aimed to analyze and visualize the scientific collaboration between Japan and Russia, using bibliometric analysis of collaborative publications from the Web of Science (WoS) database. The analysis utilized the bibliometrix package within the R statistical program. The analysis covered a period of two decades, from 2000 to 2021. The results showed a slight decrease in co-authored publications, with an annual growth rate of −1.26%. The keywords and thematic trends analysis confirmed that physics is the most co-authored field between the two countries. The study also analyzed the collaboration network and research funding sources. Overall, the study provides valuable insights into the current state of scientific collaboration between Japan and Russia. The study also highlights the importance of research funding sources in promoting and sustaining scientific cooperation between countries. The analysis suggests that more efforts in government funding are needed to increase collaboration between the two countries in various fields.