Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by core deficits in social interactions, verbal/nonverbal communication, and restricted, repetitive, and stereotyped behaviors. Children with ASD are known to have several feeding problems that are believed to affect their nutritional and health status. Aim: The present study was designed to assess the food preferences in Omani children diagnosed with ASD compared with controls. Methods: A case-control study was conducted in which 375 children (males and females) aged between 4 and 13 years were recruited. The sample consisted of 163 children with ASD and a control group of 212 typically developing (TD) children. For each participant, demographic, anthropometric, and medical information and information regarding dietary intakes were gathered using the food frequency questionnaire (FFQ) to assess their food preferences. Results: The sociodemographic characteristics of caregivers were similar in the two groups, while their perceptions based on several nutritional parameters were different. Children’s age and body mass index (BMI) were similar in both groups, while the number of male children was higher in ASD group (P < 0.001). Problematic behaviors including food refusal and selectivity were significantly higher in ASD children than in TD children. Despite that, the children with ASD were found to consume mostly traditional Omani dishes. Conclusion: This is the first study that provides information on the eating habits and nutritional intake of Omani children diagnosed with ASD. The overall findings are promising and may contribute to further understanding of food preferences in children with ASD in Oman. Such information is highly valuable for the prevention and management of nutritional deficiencies among Omani children with autism by improving their diet quality.