Epilepsy is a common disabling disease with complex, multifactorial genetic and environmental etiology. The small fraction of epilepsies subject to Mendelian inheritance offers key insight into epilepsy disease mechanisms; and pathologies brought on by mutations in a single gene can point the way to generalizable therapeutic strategies. Mutations in the PRICKLE genes can cause seizures in humans, zebrafish, mice, and flies, suggesting the seizure-suppression pathway is evolutionarily conserved. This pathway has never been targeted for novel anti-seizure treatments. Here, the mammalian PRICKLE-interactome was defined, identifying prickle-interacting proteins that localize to synapses and a novel interacting partner, USP9X, a substrate-specific de-ubiquitinase. PRICKLE and USP9X interact through their carboxy-termini; and USP9X de-ubiquitinates PRICKLE, protecting it from proteasomal degradation. In forebrain neurons of mice, USP9X deficiency reduced levels of Prickle2 protein. Genetic analysis suggests the same pathway regulates Prickle-mediated seizures. The seizure phenotype was suppressed in prickle mutant flies by the small-molecule USP9X inhibitor, Degrasyn/WP1130, or by reducing the dose of fat facets a USP9X orthologue. USP9X mutations were identified by resequencing a cohort of patients with epileptic encephalopathy, one patient harbored a de novo missense mutation and another a novel coding mutation. Both USP9X variants were outside the PRICKLE-interacting domain. These findings demonstrate that USP9X inhibition can suppress prickle-mediated seizure activity, and that USP9X variants may predispose to seizures. These studies point to a new target for anti-seizure therapy and illustrate the translational power of studying diseases in species across the evolutionary spectrum. Epilepsy is a common disabling disorder characterized by seizures with complex genetic and environmental components. The absence of a definitive pathophysiology for epilepsy stymies the development of effective treatment strategies. In a small fraction of epilepsy cases however, single gene mutations may illuminate seizure-causing mechanisms, which may open the door to the discovery of broader, more effective therapeutic strategies. We have previously shown that disruption of Prickle genes in multiple species including humans, results in a predisposition to seizures. Those findings support Prickle in a seizure-preventing role and presents a possible anti-seizure therapeutic target. We identified the deubiquitinase Usp9x (ubiquitin-specific peptidase 9 X-linked) as a new Prickle binding partner which stabilized Prickle by preventing its degradation. In mice lacking the Usp9x protein in their forebrains, Prickle2 was barely detectable. In seizure-prone prickle mutant Drosophila, reducing fat facets (Drosophila usp9x) genetically or by a small-molecule usp9x inhibitor (Degrasyn/WP1130) suppressed the seizures. We also found 2 epilepsy patients harboring mutations in USP9X. Our findings demonstrate that inhibition of Usp9x can arrest prickle-mediated seizures, and variations in USP9X may predispose to seizures. From these studies, we have elucidated a seizure-inducing mechanism, identified a potential anti-seizure target, and a potential anti-seizure drug.