Our objective was to evaluate long-term outcomes of sacral nerve stimulation (SNS) for children with functional and organic defecation disorders. We performed a prospective study of children <21 years of age who started SNS treatment between 2012 and 2018. We recorded demographics, medical history, and diagnostic testing. We obtained measures of symptom severity and quality of life at baseline and follow up at 1, 6, 12, 24, 36, 48, and ≥60 months. Successful response was defined as bowel movements >2 times/week and fecal incontinence (FI) <1 time/week. Families were contacted to administer the Glasgow Children's Benefit Inventory and to evaluate patient satisfaction. We included 65 patients (59% female, median age at SNS 14 years, range 9-21) with median follow-up of 32 months. Thirty patients had functional constipation (FC), 15 had non-retentive FI (NRFI), and 16 had an anorectal malformation (ARM). The percentage with FI <1 time/week improved from 30% at baseline to 64% at 1 year (p < 0.001) and 77% at most recent follow-up (p < 0.001). Patients with FC, NRFI, and ARM had sustained improvement in FI (p = 0.02, p < 0.001, p = 0.02). Patients also reported fewer hard stools (p = 0.001). Bowel movement frequency did not improve after SNS. At most recent follow-up, 77% of patients with a functional disorder and 50% with an organic disorder had responded (p = 0.03). Nearly all families reported benefit. SNS led to sustained improvement in FI regardless of underlying etiology, but children with functional disorders were more likely to respond than those with organic disorders.