Autism spectrum disorder (ASD) is a diverse group of neurodevelopmental conditions with complex origins. Individuals with ASD present various neurobiological abnormalities, including an altered immune response in the central nervous system and other tissues. Animal models like the C58/J inbred mouse strain are used to study biological characteristics of ASD. This strain is considered an idiopathic autism model because of its demonstrated reduced social preference and repetitive behaviours. Notably, C58/J mice exhibit alterations in dendritic arbour complexity, density and dendritic spines maturation in the hippocampus and prefrontal cortex (PFC), but inflammatory‐related changes have not been explored in these mice. In this study, we investigated proinflammatory markers in the hippocampus and PFC of adult male C58/J mice. We discovered elevated levels of interferon gamma (IFN‐γ) and monocyte chemoattractant protein 1 (MCP‐1) in the hippocampus, suggesting increased inflammation, alongside a reduction in the anti‐inflammatory enzyme arginase 1 (ARG1). Conversely, the PFC displayed reduced levels of TNF‐α and MCP‐1. Microglial analysis revealed higher levels of transmembrane protein 119 (TMEM119) and increased microglial density in a region‐specific manner of the autistic‐like mice, particularly in the PFC and hippocampus. Additionally, an augmented expression of the fractalkine receptor CX3CR1 was observed in the hippocampus and PFC of C58/J mice. Microglial morphological analysis shows no evident changes in the hippocampus of mice with autistic‐like behaviours versus wild‐type strain. These region‐specific changes can contribute to modulate processes like inflammation or synaptic pruning in the C58/J mouse model of idiopathic autism.