Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by deficits in social interaction, communication, restricted interests, and repetitive behaviors. Its higher prevalence in males underscores the importance of understanding potential sex-specific differences. Prenatal exposure to valproic acid (VPA) is a widely used preclinical model to induce ASD-like traits in rodents; however, few studies have systematically compared neurobehavioral outcomes in both sexes. Here, we aimed to investigate sex-specific variations in developmental, behavioral, and physiological parameters in Wistar rat offspring prenatally exposed to VPA. Pregnant rats received a single intraperitoneal injection of VPA (600 mg/kg) or saline on gestational day (GD) 12.5, and offspring were assigned to four groups: control males, control females, VPA males, and females (n = 9 per group). VPA-exposed rats of both sexes exhibited autism-like behaviors, including heightened anxiety, increased exploratory activity, repetitive behaviors, social deficits, spatial and recognition memory impairments, and depressive-like traits. Physiological assessments revealed altered gastrointestinal (GIT) motility, increased brain edema, impaired blood-brain barrier (BBB) function, and neuronal injury with no sex-based difference in estrogen β (ERβ/ESR2) mRNA expression. These findings demonstrate that in utero exposure to VPA induces autism-like behaviors, developmental abnormalities, and neurodegenerative changes in both rat sexes, emphasizing the importance of including females in preclinical ASD research.