The two most common genetic developmental disorders that cause intellectual disability are Down syndrome (DS) and Fragile X syndrome (FXS). Although the genetics and behavioral hallmarks of these two disorders are distinct, common underlying defects in neural development may lead to the cognitive impairment characteristic of both. Human neural progenitor cells (hNPCs) enable the study of prenatal human brain development in these developmental disorders. We therefore tested whether there are common affected molecular pathways in FXS and DS hNPCs that may be indicators of the fundamental developmental causes of intellectual disability. Comparison of gene expression data from FXS and DS (disorder group) hNPCs to unaffected hNPCs indicated genes in specific signal transduction cascades are dysregulated. Importantly, altered expression of genes in these signaling pathways did not emerge when the two disorder hNPCs were analyzed separately. Specifically, genes in the mitogen-activated protein kinases (MAPK/ERK) and calcium signaling pathways are mis-expressed in disorder hNPCs. These results suggest that DS and FXS hNPCs do not communicate or respond appropriately to extracellular cues during neural development. These results validate the use of hNPCs as a tool to assess complex cell functions during neural development and suggest that defects in the pathways identified could have profound effects on how neural progenitor cells survive, proliferate and differentiate, thereby leading to intellectual disability.