Many patients with anorectal malformations (ARM) need a bowel management program (BMP) to manage lifelong problems of fecal incontinence or severe constipation. We aimed to evaluate the sustainability of the results in such a program. A single-institution retrospective review was performed in children with ARM who attended our BMP (2015-2019). Standardized definitions and validated tools were used to assess fecal continence (Baylor Continence Scale), constipation (Cleveland Constipation Scoring System), urinary symptoms (Vancouver Symptoms Score), and the Pediatric Quality of Life (PedsQL) and health-related quality of life (HRQOL) at the start of BMP and 1-year after completion of the program. 222 patients with ARM at a median age of 6.7 (IQR, 4.9-10.1) years were identified. All (100%) soiled at intake with 149 (67.1%) patients being treated with rectal or antegrade enemas and 73 (32.9%) with oral laxatives. At 1 year 150 (70.4%) were clean, 72.7% were on enemas and 27.3% were on laxatives (p = 0.08). 109 out of 148 (73.6%) patients were clean on enemas. A further 41 out of 66 (62.1%) patients were continent on laxatives with voluntary bowel movements and clean. In the group that was clean, there was improvement in Baylor Continence Scale (25 vs. 13.0, p < 0.000000002), Vancouver (11 vs. 6, p = 0.0110) scores, and clinically relevant improvement in the total PedsQL HRQL (78-85) and the PedsQL HRQL physical function (86-92) and psychosocial domain (77-82). There was no improvement in Cleveland (10 vs. 9, p = 0.31) score. An intensive BMP offers significant benefits in the treatment of fecal incontinence in ARM. It appears to also improve urinary incontinence and urinary voiding as well as the patient's quality of life. These changes are sustainable over at least one year.