To compare the effectiveness of pelvic floor interferential (IF) therapy with trans-abdominal IF therapy in children with intractable functional constipation. Information of 64 children (38 boys, 26 girls; mean age: 6.6 ± 2.2) with functional constipation who had been treated with IF therapy were considered for this retrospective study. Group A (n = 32) underwent pelvic IF electrical stimulation + pelvic floor muscle (PFM) exercises while the group B (n = 32) received transabdominal IF therapy + PFM exercises. A complete bowel habit diary, a constipation score questionnaire and a seeable pain scores had been recorded before, after the ending of treatment courses and six months later for children in both groups. Additionally, children had been assessed with a constipation-related quality of life questionnaire before and six months after treatment. The number of patients who compiled the diagnostic criteria for constipation significantly decreased in both groups after treatment, in which 27/32 (84.3%) of patients in each group had no constipation after the ending of therapy courses (P = 1). Fecal soiling episodes reduced in both groups after treatment, this finding was significantly higher in group A than in group B after the ending of therapy courses (P = 0.05) and six months later (P = 0.01). Results of this study showed that using IF therapy both pelvic floor and transabdominal significantly boosts the effects of treatment among patients with functional constipation. Pelvic floor IF therapy is more effective in patients who had concomitant fecal soiling.