BackgroundAvailability and accessibility of anti-cancer medicines is the pillar of cancer management, and it is one of the main concerns in low-income countries including Rwanda. The objective of this study was to assess the availability and affordability of anticancer medicines at cancer-treating hospitals in Rwanda.MethodologyA descriptive cross-sectional study was conducted at 5 cancer-treating hospitals in Rwanda. Quantitative data were collected from stock cards and software that manage medicines and included the availability of anti-cancer medicines at the time of data collection, their stock status within the last two years, and the selling price.ResultsThe study found the availability of anti-cancer medicines at 41% in public hospitals at the time of data collection, and 45% within the last two years. We found the availability of anti-cancer medicines at 45% in private hospitals at the time of data collection, and 61% within the last two years. 80% of anti-cancer medicines in private hospitals were unaffordable while 20% were affordable. The public hospital that had most of the anti-cancer medicines in the public sector provided free services to the patients, and no cost was applied to the anti-cancer medicines.ConclusionThe availability of anti-cancer medicines in cancer-treating hospitals is low in Rwanda, and most of them are unaffordable. There is a need to design strategies that can increase the availability and affordability of anti-cancer medicines, for the patients to get recommended cancer treatment options.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12913-023-09706-y.