This study focused on the effect of Risk Based Audit Approach (RBAA) on internal control systems in government departments in Uasin Gishu County, Kenya. In spite of the gains realized by RBAA, external auditors have continually issued qualified reports with regards to unsupported expenditure, non-updated bank reconciliation, pending bills, poor expenditure control and unsurrendered imprests warrants. The objectives of this study were to establish the RBAA strategies used in implementing internal control activities in government departments in Uasin Gishu County, to examine the extent to which RBAA has influenced the implementation of internal control activities in government departments in Uasin Gishu County and finally to establish the challenges encountered by RBAA in implementing internal control activities in government departments in Uasin Gishu County.