This study aimed to explore the effect of auditory integration therapy (AIT) on the forkhead box J1 protein and assessed its impact on behavioral, social, and sensory symptoms in children with autism. Behavioral, social, and sensory scores were calculated for each child using the childhood autism rating scale, social responsiveness scale, and short sensory profile before and after AIT. The plasma level of Foxj1 was [575 (351-2553) pg/mL] [median (interquartile range)] before AIT. This level did not change significantly (p˃0.05) immediately [1143(336-4599)], after one month [1268 (275-4932)], or three months [1058 (184-3462)] AIT. However, results revealed that behavioral, social, and sensory rating scales were improved after AIT. Pearson correlation (r) values before and after AIT between severity variables were calculated. Unchanged plasma levels of Foxj1 after AIT supported the non-therapeutic effect of AIT on Foxj1 in autistic children. A significant change in behavioral, social, and sensory symptoms was noticed in autistic children. Additional research, on a large population, is necessary to assess AIT's impact on behavioral and social changes in children with an autism spectrum disorder.