To investigate associations between the rectoanal inhibitory reflex (RAIR), type of congenital anorectal malformations (ARMs), type of operation that patients with ARM had undergone, and objectively measured fecal incontinence and defecation problems. We retrospectively included 69 pediatric patients with ARM. All underwent anorectal function tests at the University Medical Center of Groningen during the last 10 years. We assessed anorectal physiology using the Rome IV criteria and anorectal function tests. We found the reflex in 67% of patients and all types of ARMs. All patients who had not been operated on, and those who had undergone less extensive surgery possessed the reflex. In contrast, patients who underwent posterior sagittal anorectoplasty, 44% possessed it. We found no difference between mean rectal volumes in patients with and without the reflex (251 vs. 325 mL, respectively, p = 0.266). We found that over time, patients without the reflex seemed to develop significantly higher rectal volumes than patients who had it. We did not find a significant difference between the reflex and fecal incontinence; however, it seems that the absence of the reflex, resting anal sphincter pressure, and fecal incontinence are related. The RAIR seems present in patients with ARM irrespective of their malformation type. Corrective surgery, however, may impair this reflex. Seemingly, its absence results in constipation with enlarged rectal volumes and fecal incontinence. Every effort should be made to preserve this reflex during surgery and to use extensive surgical procedures as sparingly as possible.