Background/Objectives: Autism is a complex neurodevelopmental condition characterized by social and cognitive impairments, with growing evidence implicating neuroinflammation, disrupted autophagy, apoptosis, GABAergic dysfunction, and gut permeability in its pathophysiology. Thus, this study aimed to evaluate the independent and combined effects of intermittent fasting (IF) and the next-generation probiotic Akkermansia muciniphila on behavioral outcomes and molecular markers in prenatal valproic acid (VPA)-induced autism model. Methods: Male rat offspring were allocated into five groups (n = 8 per group): control, VPA, IF, probiotic, and IF + probiotic. The groups other than the control group were exposed to 500 mg/kg VPA prenatally to establish an autism model. Intermittent fasting (16:8 time-restricted feeding) and Akkermansia muciniphila (1 × 10⁹ cfu/day) were applied for 30 days. Behavioral tests (stereotypy, social interaction, memory, and anhedonia) were performed during the last eight days of the treatment period, and the rats were sacrificed the following day for collection of brain tissue and serum samples. Proinflammatory, apoptotic, autophagic, and GABAergic markers were measured in the prefrontal cortex and hippocampus, while zonulin levels were measured in the serum. Data were analyzed using one-way ANOVA followed by Tukey’s post-hoc test. Results: Prenatal VPA exposure worsened all behavioral and molecular parameters. All treatments improved stereotypy, social interaction, and memory, whereas anhedonia improved only in the combined treatment group. The treatments also decreased neuroinflammation and apoptosis-related imbalance while enhancing autophagy and GABAergic markers. In terms of apoptosis- and autophagy-related markers, the IF-only and probiotic-only treatments were effective in the prefrontal cortex, while the IF + probiotic treatment showed its effect in both brain regions. Lastly, all treatments were successful in alleviating elevated serum zonulin levels. Conclusions: Intermittent fasting and Akkermansia muciniphila alleviate VPA-induced behavioral and neurobiological impairments. The combined treatment, in particular, offers stronger and multi-targeted therapeutic potential.