Background and objectives This study aimed to explore the frequency of gastrointestinal (GI) symptoms and associated risk factors among children with autism spectrum disorder (ASD). Methods This was a retrospective case-control study including children aged 2-14 years diagnosed with ASD by the Diagnostic and Statistical Manual of Mental Disorders (DSM)-5 criteria and the assessment card in the ASD center at King Salman Armed Forces Hospital. Data were obtained using a self-developed questionnaire that included demographic features, nutritional and behavioral characteristics, and GI symptoms in the previous six months. The control group consisted of typically developing (TD) children matched to the ASD group for age and gender. Syndromic autism with defined somatic abnormalities and recognized genetic causes (e.g., fragile X syndrome, tuberous sclerosis) were excluded Results A total of 146 ASD children and 114 normal children were included. No significant demographic differences were found between the groups. The ASD group had a higher frequency of low income and a significantly lower rate of exclusive breastfeeding in the first six months. GI symptoms, specifically constipation, abdominal gases and distension, diarrhea, undigested food particles in stool, and mouth ulcers, were significantly more frequent in the ASD group. Weight abnormalities (both increase and decrease) were also more common. Family history of ASD was significantly more in ASD children with GI symptoms while low maternal education was more in those without. Conclusion This study reveals a high prevalence of GI symptoms in ASD children. Family history of ASD and maternal education may influence the GI symptoms reported in ASD children.