Concerns over misappropriation and misuse of Free Primary Education funds have been raised by parents, the government and donors despite the increased funding. It is not clear the extent of use of internal control procedures in public primary schools are contributing to this state of affairs. Therefore, the purpose of this study was to establish the effectiveness of internal control procedures on management efficiency of FPE funds in public primary schools in Kisii Central District. The study was guided by the stewardship theory which advocates for integrity, transparency and accountability. The study targeted 267 respondents comprising of 132 head teachers, 132 SMCs chairpersons and 3 District Education staff in Kisii Central District, Kisii County, from which a random sample of 117 was taken for study. The findings of the study revealed that use of internal control procedures are effective on management efficiency of funds in schools and therefore recommends embracing enhanced internal control procedures in their resolve to efficient management.