The aims of this study were to record behavioral problems in children with epilepsy (CWE), compare the prevalence with that reported among healthy children without epilepsy, and investigate the risk factors. A child behavioral questionnaire for parents comprising 15 items was administered to the main caregiver of 108 CWE and 108 controls matched for age in Kilifi, Kenya. CWE had a higher mean score for reported behavioral problems than controls (6.9 vs 4.9, t=4.7, P<0.001). CWE with active epilepsy also recorded more behavioral problems than those with inactive epilepsy (8.2 vs 6.2, t=-2.9, P=0.005). A significantly greater proportion of CWE (49% vs 26% of controls) were reported to have behavioral problems. Active epilepsy, cognitive impairment, and focal seizures were the most significant independent covariates of behavioral problems. Behavioral problems in African CWE are common and need to be taken into consideration in planning comprehensive clinical services in this region.