Mutations in the X-linked cyclin-dependent kinase like 5 gene (CDKL5) cause a severe neurodevelopmental disorder (OMIM300672) referred to as CDKL5 deficiency disorder (CDD). CDD patients are characterized by early-onset drug-resistant epilepsy, intellectual disability, and autistic-like features. No cure exists for CDD patients, and the development of drug-based therapies is still extremely challenging due to the limited knowledge of CDKL5 functions. While CDKL5 has a well-known role in excitatory neurotransmission, its functions in the inhibitory compartment are still poorly characterized. To fill this gap, we have explored a potential role of CDKL5 in the inhibitory compartment in Cdkl5-KO mice and primary hippocampal neurons. We show that CDKL5 loss in primary hippocampal neurons leads to reduced surface expression of synaptic GABAARs, which is accompanied by a decrease in the frequency of miniature inhibitory postsynaptic currents. Molecularly, these results may be explained by the interaction of CDKL5 with collybistin and gephyrin. Gephyrin is a postsynaptic scaffolding protein essential for GABAAR clustering, while collybistin is a brain specific GEF regulating the submembrane distribution of gephyrin thanks to its alternating between a folded inactive and an open extended conformation. Intriguingly, using a heterologous system, we show that CDKL5 can induce the active conformation of collybistin, thus inducing the submembrane clustering of gephyrin. The impact of CDKL5 loss on inhibitory synapses was confirmed also in hippocampi of Cdkl5-KO mice. Considering the recently outlined role of CDKL5 in regulating microtubule (MT) dynamics, which are involved in receptor trafficking, we tested the effect of a neurosteroid promoting MT dynamics and found a robust restoration of all CDKL5-dependent inhibitory defects. Our results may help elucidating the molecular mechanism of the cognitive features and epilepsy in CDD patients and developing disease-modifying therapies.