Polyunsaturated fatty acids (PUFAs) are essential for brain development and function. Increasing evidence has shown that an imbalance of PUFAs is associated with various human psychiatric disorders, including autism and schizophrenia. Fatty acid-binding proteins (FABPs), cellular chaperones of PUFAs, are involved in their intracellular trafficking, signal transduction, and gene transcription. We previously demonstrated that FABP3 is robustly expressed in the GABAergic inhibitory interneurons in the medial prefrontal cortex (mPFC) of both juvenile and adult wild-type mice. Although the expression of FABP3 becomes evident after birth, the function of FABP3 is largely unknown in postnatal brain. In particular, the effects of FABP3 deletion in the mPFC GABAergic inhibitory interneurons are unclear. In this study, we comprehensively investigated the changes in gene expression due to the presence or absence of FABP3 in the mPFC at postnatal day 24 (P24), when FABP3 expression shows its highest value. We isolated nuclei from ｔhe mPFC of wild-type and FABP3 gene knockout mice and conducted single-cell RNA sequencing. Focusing on the GABAergic inhibitory interneurons, we identified numerous genes with differential expression in gene groups involved in brain development, adult behavior and regulation of neuron differentiation. These results suggest that FABP3 is involved in the development of inhibitory synapse in the mPFC.