Purpose: Modifying gut bacteria in children with autism may influence behaviour, with potential to improve family functioning. We conducted a randomised controlled trial to assess the effect of prebiotics on behaviour, gastrointestinal symptoms and downstream effects on parental quality of life. Method: Children with autism (4-10yrs) were randomised to 2.4 g/d of prebiotic (GOS) or placebo for six weeks. Pre and post stools samples were collected, and validated questionnaires used to measure change in social and mealtime behaviours, GI symptoms and pQOL. Linear mixed models evaluated group differences for behavioural variables, and Mann Whitney U tests were used to compare change between-groups for GI symptoms, differential abundance of genera and alpha diversity of the microbiome. Results: Thirty-three parent-child dyads completed the trial. No group difference was seen for behavioural variables but both groups improved significantly from baseline. There was a medium effect size between groups for GI symptoms (d = 0.47) and pQOL (d = 0.44) driven by greater improvements in the prebiotic group. Bifidobacterium increased threefold following prebiotics (1.4-5.9%, p < 0.001) with no change in controls. Supplements were well tolerated, compliance with dose 94%. Conclusion: Prebiotics modify levels of "Bifidobacterium" and prove well tolerated but in this instance, resulted in only marginal effects on GI symptoms and pQOL. A larger sample of children with more severe symptoms could help to determine the potential of prebiotics in autism.