Children with autism spectrum disorder (ASD) are often delayed in achieving bowel continence, resulting in negative outcomes. In this pilot trial, 20 children with ASD and encopresis were randomly assigned to multidisciplinary intervention for encopresis (MIE; n = 10) or a waitlist control group (n = 10). The MIE group was treated for constipation and received a 10-day behavioral intervention that utilized suppositories to produce predictable bowel movements that were reinforced. Caregivers were trained to implement the intervention. Results support the feasibility of clinical trials of MIE, with high enrolment, competition, attendance, and caregiver acceptability. Preliminary outcomes were positive, with six of 10 in the MIE group achieving continence by the end of treatment compared to 0 in the control group ( p  = 0.005). Registered at clinicaltrials.gov ( https://clinicaltrials.gov ); ID: NCT02383732.