SLC13A5 encodes a citrate transporter highly expressed in the brain and is important for regulating intra- and extracellular citrate levels. Mutations in this gene cause rare infantile epilepsy characterized by lifelong seizures, developmental delays, behavioral deficits, poor motor progression, and language impairments. SLC13A5 individuals respond poorly to treatment options; yet drug discovery programs are limited due to a paucity of animal models that phenocopy human symptoms. Here, we used CRISPR/Cas9 to create loss-of-function mutations in slc13a5a and slc13a5b, the zebrafish paralogs to human SLC13A5. slc13a5 mutant larvae showed cognitive dysfunction and sleep disturbances, consistent with SLC13A5 individuals. These mutants also exhibited fewer neurons and a concomitant increase in apoptosis across the optic tectum, a region important for sensory processing. Further, slc13a5 mutants displayed hallmark features of epilepsy, including an imbalance in glutamatergic and GABAergic excitatory-inhibitory gene expression, increased fosab expression, disrupted neurometabolism, and neuronal hyperexcitation as measured in vivo by extracellular field recordings and live calcium imaging. Mechanistically, we tested the involvement of NMDA signaling and zinc chelation in slc13a5 mutant epilepsy-like phenotypes. Slc13a5 protein co-localizes with excitatory NMDA receptors in wild-type zebrafish and NMDA receptor expression is upregulated in the brain of slc13a5 mutant larvae. Additionally, low levels of zinc are found in the plasma membrane of slc13a5 mutants. NMDA receptor suppression and ZnCl2 treatment in slc13a5 mutant larvae rescued neurometabolic and hyperexcitable calcium events, as well as behavioral defects. These data provide empirical evidence in support of the hypothesis that excess extracellular citrate over-chelates the zinc ions needed to regulate NMDA receptor function, leading to sustained channel opening and an exaggerated excitatory response that manifests as seizures. These data show the utility of slc13a5 mutant zebrafish for studying SLC13A5 epilepsy and open new avenues for drug discovery.