There is little evidence that implementations of Electronic Medical Record Systems (EMRs) are associated with better reporting completeness and timeliness of HIV routine data to the national aggregate system. We analyzed the reporting completeness and timeliness of HIV reports to Kenya's national aggregate reporting system from District Health Information Software 2 (DHIS2) for the period 2011 to 2018. On average, reporting completeness improved to 97% whilst timeliness increased to 83% in 2017 with similar performance for the facilities under study that implemented either KenyaEMR or IQCare. However, in 2018, the reporting rates dropped by 13% for completeness and 11% for timeliness most likely due to changed reporting procedures. This suggests that besides EMRs, there are other factors influencing reporting such as reporting routines, which need to be assessed separately. Nonetheless, the EMRs have facilitated the collection of HIV data for submission to the DHIS2, which in turn facilitates the reporting process for the data officers.