Background We compared the effects of transcutaneous functional electrical stimulation (TFES) and biofeedback therapy with TFES alone in a cohort of children with functional non-retentive fecal incontinence (FNRFI). Methods This prospective, single-center randomized clinical trial was performed on 40 children with FNRFI. Patients were randomly allocated into two equal treatment groups. Group A ( n  = 20) underwent TFES + biofeedback therapy, and group B ( n  = 20) received TFES alone. All patients were assessed with a pediatric fecal incontinence (FI) score questionnaire, a visual pain score, and a bowel habit diary both before and at the end of treatment sessions and also at 6 months of follow-up. In addition, a FI quality-of-life (QoL) questionnaire was recorded for all patients before and 6 months after the treatment. Results FI significantly improved in 13/20 (65%) patients in group A and 11/20 (55%) patients in group B ( P  < 0.05). A significant reduction in FI score was seen in each group at the end of treatment sessions and maintained at 6 months of follow-up ( P  < 0.05). A significant improvement in FI-QoL scores was seen in both groups at 6 months of follow-up in which there was no significant difference in terms of FI-QoL scores improvement between both groups after treatment. Conclusions The use of electrical stimulation in combination with other treatment methods improves symptoms in patients with FNRFI who are refractory to conventional treatment.