Introduction Due to the commitment by the Government of Kenya (GoK) and international donors to address HIV/AIDS, Kenya has some of Africa's most developed health infrastructure for tackling the crisis. Despite this commitment, significant gaps exist in the national HIV/AIDS monitoring and evaluation (M&E) system. To identify these gaps and opportunities for improvement, the U.S. Centers for Disease Control and Prevention funded the Strengthening HIV Strategic Information in Kenya project, which conducted an organizational HIV M&E capacity rapid needs assessment (RNA). Methods The project included an in-depth desk review of national documents, policies, tools, and international best practices. National, regional, and district officials from government agencies, development partners, and implementing partners participated in key informant interviews and focus group discussions. Given the large number of regions and districts, purposive sampling was used to select 16 facilities in 8 districts across 2 regions based on the general quality of the reported HIV data and the number of partners supporting the regions. Results RNA findings revealed tremendous improvements at the national level and in the various subsystems that contribute to the overall HIV strategic information. There also were significant gaps, including in a lack of M&E guidelines, parallel reporting systems, feedback given to subnational levels, and data use and general data management and use capacity at subnational levels. Conclusion An urgent need exists for the development of national M&E guidelines and a comprehensive training curriculum. To ensure success further, capacity building for subnational levels should be conducted and feedback channels to subnational staff should be established and maintained.