Developmental and Epileptic Encephalopathy 9 (DEE9, OMIM # 300088) is a debilitating neurological condition with no effective cure, characterized by early-onset seizures, intellectual disability and autism. DEE9 mainly affects females and is due to mutations in the X-linked gene PCDH19, which cause mosaic loss of PCDH19 function. PCDH19 encodes protocadherin-19 (PCDH19), a calcium-dependent cell adhesion molecule highly expressed in the limbic system, whose function is still largely unknown. Our in vitro studies showed that PCDH19 is a multifaceted protein with a role in both synapses and the nucleus. At inhibitory synapses, PCDH19 modulates GABAergic transmission through its interaction with GABAA receptors. At excitatory synapses, PCDH19 undergoes a NMDA receptor (NMDAR)-dependent proteolytic processing, which enables information transfer to the nucleus and epigenetic regulation of gene expression. To study PCDH19 function in vivo, we generated a conditional KO mouse model able to mimic mosaic expression of PCDH19 and to recapitulate key behavioral traits of DEE9. Patch-clamp experiments on brain slices revealed that PCDH19-negative neurons within the hippocampus of mosaic mice forms a pool of hyperexcitable cells. Overall, excitatory synaptic density is reduced, and hippocampal synapses display altered structure and plasticity in these mice. At network level, PCDH19 mosaic expression leads to a global reduction of firing rate associated with increased neuronal synchronization, as inferred from multielectrode array recordings. Furthermore, neuronal network analysis in freely behaving mosaic mice revealed a decrease in excitatory/inhibitory ratio and functional hyperconnectivity within the limbic system. Altogether, these results indicate that PCDH19 mosaic expression profoundly affects circuit wiring and functioning and provide new key to interpret DEE9 pathogenesis.