Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by impaired social communication, restricted interests, repetitive behavior and irritability. Exposure to valproic acid (VPA) during pregnancy has been shown to increase the risk of autism in children and has led to the development of the in-utero VPA rat model that elicits neurodevelopmental autistic-like features. Offspring exhibit behavioral and neurobiological alterations modelling ASD symptoms. We performed a behavioral and molecular assessment in a rat in-utero VPA model treated with a novel botanical cannabinoid, JZP541. Male offspring from dams treated with VPA were tested acutely and sub-chronically with JZP541 (10, 30, or 100 mg/kg, intraperitoneally). A behavioral testing battery was performed, and brain frontal cortex and hippocampus used for RNA sequencing. In utero exposure to VPA resulted in progeny showing behavioral phenotypes characteristic of ASD. JZP541 attenuated these deficits in social, stereotypic, hyperactivity and irritability behavior in a dose-dependent fashion. VPA exposure was associated with a substantial transcriptional dysregulation impacting multiple key biological processes in a tissue-dependent manner. The expression profiles were integrated with publicly available datasets of autism-associated genes to support the validity of the model used and to focus on the effects of treatment on known autism-relevant transcriptional targets. This approach indicated a strong and dose-dependent reduction of the autism-associated gene expression signature in brain samples from animals dosed with JZP541. Our findings demonstrate JZP541 was able to ameliorate ASD associated behavioral deficits, and this was supported by improvements in putative transcriptional biomarkers of ASD.