Congenital hydrocephalus (CH) is a complex neurodevelopmental disorder characterized by enlarged brain ventricles and reduced cognitive functions. Here, we identified FLVCR1a (Feline Leukemia Virus Subgroup C Receptor 1) as a novel gene responsible for CH in humans. However, the molecular mechanism linking FLVCR1 loss to neurodevelopmental defects is still elusive. To clarify this, we generated mice lacking Flvcr1a in neural progenitor cells (NPCs) by using rat-Nestin promoter CRE model (NesCRE). Interestingly, the FLVCR1a fl/fl-NesCRE+ model recapitulates the main features of the human disease, showing enlarged embryo brain ventricles. Phenotypic analyses of FLVCR1a fl/fl-NesCRE+ embryo brains showed impaired neurogenesis and reduced NPCs proliferation. To better dissect the molecular mechanism, we used Tandem Affinity Purification (TAP) strategy coupled to mass spectrometry to study FLVCR1a interactome. Our data reveal that FLVCR1a interacts with the IP3R3-VDAC complex controlling mitochondrial calcium handling. Interestingly, mitochondrial calcium is essential for the maintenance of proper cellular bioenergetics and it is emerging as an essential factor for NPC proliferation. Therefore, we investigated whether altered mitochondrial calcium influx is present in NPCs derived from FLVCR1a fl/fl-NesCRE+ embryos. We found that Flvcr1a loss in NPC severely impair mitochondrial calcium and subsequently, bioenergetics. Notably, mitochondrial Ca2+ uptake restoration rescues the metabolism and proliferation of NPC lacking Flvcr1a. In conclusion, these findings support a previously undescribed role of FLVCR1a in the regulation of ER-mitochondria membrane tethering and mitochondrial calcium transfer through its interaction with the IP3R3-VDAC complex, suggesting defective NPC calcium handling and metabolic activity as one of the pathogenetic mechanisms driving CH.