The cerebral cortex and hippocampus are important for the control of cognitive functions and social behaviors. Cortical and hippocampal dysfunction has been observed in a variety of neurological diseases and psychiatric disorders, many of which display gender bias in incidence and symptomatology, including autism and Alzheimer's disease. Some of these sex‐biased diseases have been linked to defects in pre‐mRNA splicing, suggesting that RNA processing factors may play a vital role in brain sexual differentiation at the posttranscriptional level. Therefore, we hypothesize that the expression of the genes associated with RNA splicing and processing might be sexually dimorphic in the mouse cortex and hippocampus during early development, which creates different mRNA variants between the sexes and then leads to differences in structure and function of these brain regions. To test our hypothesis, we first reanalyzed our gene expression microarray data in neonatal mouse cortex/hippocampus with Gene Ontology enrichment analysis and found that the genes with the annotation of “RNA binding” were over‐represented (13 out 89 candidate genes). With addition of 4 other genes with the same annotation displaying >1.2‐fold difference in expression between the sexes, we identified 17 candidate genes. We next used reverse transcriptase with quantitative PCR (RT‐qPCR) to measure and determine relative mRNA levels of the 14 candidate genes residing autosomal chromosomes in the cortex/hippocampus of male and female mice collected on the day of birth (PN0), and 7 (PN7), 14 (PN14), and 21 (PN21) days after birth. A two‐way ANOVA revealed a significant main effect of sex on mRNA levels of Khdrbs2, Nanos2, Rbm48, and Tdrd3. Among these genes, females expressed more Rbm48 and Tdrd3 mRNA on PN0 and PN7 while female‐biased Khdrbs2 expression was observed in neonates. In contrast, Nanos2 displayed an overall female‐biased expression among all ages, but there was no significant effect of sex on mRNA levels at a particular age. These results suggest that sex and age‐dependent change in expression of RNA processing factors might be the molecular mechanism underlying the development of sexual dimorphism in cortical and hippocampal structure and function as well as gender bias in risk and resilience to neurological diseases and psychiatric disorders associated with these brain regions.