Over 400 mutations have been identified as contributors to inborn errors of immunity (IEI). Although IEI patients are primarily treated for immunodeficiency, an increasing number of reports have suggested that neurodevelopmental deficits (NDDs) may also be a co-morbidity of IEI. However, the mechanisms by which typically immune mutations could potentially increase NDD risk are currently unknown. To investigate this, we explored whether an overlap between IEI and NDD susceptibility genes existed, and evaluated which pathways were affected by these genes. Data mining of the HGMD and the IUIS gene list revealed that ~1/3 of IEI risk genes overlapped with NDD risk genes. Analysis of Human Protein Atlas RNAseq data showed a progressive gene expression pattern between immune and brain tissue: a higher number of NDD-only genes was found in brain cells, followed by shared and IEI-only genes, a pattern that was inverted in immune cells. Linear discriminant analysis separated the three gene groups based on expression patterns, and revealed that IEI-only and shared groups were primarily differentiated by immune tissue expression profiles. Gene ontology analysis identified “immune function” as a high-scoring process in both groups of genes, while biological grouping indicated that shared genes were primarily involved in immune cell differentiation and development and IEI-only genes in immune activation and response. This analysis suggests that distinct IEI mutation groups could potentially differentiate patients into high/low-neurodevelopmental disorder risk. The genetic overlap between immune and neurodevelopmental genes suggests that NDDs could be underdiagnosed in IEI patients.