Decision makers are searching for reliable data and best practices to support the implementation and scale-up of the integrated community case management (iCCM) programs in underserved areas to reduce under-five mortality in low-income countries. This study assesses data quality and reporting systems of the World Health Organization supported Rapid Access Expansion program implementing iCCM in Abia and Niger States, Nigeria. This cross-sectional study used data from 16 primary health facilities in both states. Data were collected through review of registers and monthly summary reports of 140 community-oriented resource persons (CORPs), assessments of the five dimensions of the data reporting systems and 46 key informant interviews with stakeholders. Data quality was assessed by availability, completeness and consistency. Each component of the reporting system was assessed on a 3-point scale (weak, satisfactory and strong). Results show that both the structure, functions and capabilities, as well as data collection and reporting tools dimensions of the reporting system were strong, scoring (2.80, 2.73) for Abia and (2.88, 2.75) for Niger, respectively. Data management processes and links with national reporting system components scored low 2 s, indicating fair strength. Data availability, completeness and consistency were found to be good, an indication of adequate training and supervision of CORPs and community health extension workers. Indicator definitions and reporting guidelines were the weakest dimension of the system due to lack of data reporting guidelines in both states. In conclusion, the results indicate satisfactory data reporting systems and good quality data during early implementation of iCCM programs in the two states. Hence, countries planning to adopt and implement iCCM programs should first develop structures, establish national standardized tools for collecting and reporting data, provide for adequate training and supervision of community health workers and develop reporting guidelines for all reporting levels to ensure data quality.