Abstract: The generation of health information starts at the community level through the Community-Based health information system. At the community level, this source of information is complete in coverage and in planning and action-oriented (Odhiambo-Otieno, 2005). The objective of the study was to assess the internal and external factors influencing the functionality of CBHIS in Embakasi Sub-County, Nairobi County, Kenya. The study was descriptive cross sectional in nature where both qualitative and quantitative methods of data collection were used. The study adopted Key Informants interview, for link health facility workers, and 2 sets of questionnaires for Community Health Unit workers. The data/reporting tools, feedback forums, training and support supervision were available but inadequate and that CHUs did not have data analysis capacity. The community was very supportive to CHUs activities and the linkages were effective as stated by all the respondents. Challenges that were said to face the linkages included; community health workers shortage, inadequate tools, inconsistent indicators and late reporting. However 3(60%) of the CHEWs pointed out that the county leadership was unsupportive to the CHUs while 2(40%) reported the county leadership supportive. The researcher recommend that the local leadership should provide the workers with adequate tools, capacity build them on data analysis, strengthen dialogue and action days, offer frequent refresher training and equip the workers with supervisory skills. The linkages between CBHIS and FHIS should be strengthened and that the local leadership should support the community health unit activities.