Background <p>Children with congenital colorectal conditions require care from multiple health professionals. However, evidence on the value of a multidisciplinary care model is lacking. This study aimed to elicit public preferences and willingness to pay for a multidisciplinary care model for children with congenital colorectal conditions.</p> Methods <p>We developed a discrete choice experiment (DCE) that was administered to 807 members of the Australian public online. A Bayesian D-efficient design consisting of 20 choice tasks was split into 2 blocks of 10 choice tasks per respondent. Five attributes elicited through mixed methods included make-up of the multidisciplinary team; responsibility for care coordination; duration of access; provision of educational information; and cost. Choice data were analysed with a panel error component mixed logit model. Willingness to pay for each DCE attribute and level was estimated using the unconditional population moments estimates.</p> Results <p>The Australian public demonstrated preference for a multidisciplinary care model. They showed preference for long-term access, having a care coordinator and provision of additional information. The public was willing to pay Australian dollars (AU) $64,275 for a multidisciplinary care model comprising an essential multidisciplinary team (including a surgeon, clinical nurse consultants, a psychologist, a social worker, stomal therapists, a child life therapist and a dietitian) with care coordination and information booklets and ongoing care until the child reached adulthood. We observed preference heterogeneity associated with gender, parenthood status and household income.</p> Conclusions <p>The Australian public valued the multidisciplinary care model for children with complex colorectal conditions. Our findings can be used to inform the design of a multidisciplinary care model and to inform cost–benefit analyses as part of broader healthcare system implementation.</p>