Bmcc1s, a brain-enriched short isoform of the BCH-domain containing molecule Bmcc1, has recently been shown to interact with the microtubule-associated protein MAP6 and to regulate cell morphology. Here we identified kidney-type glutaminase (KGA), the mitochondrial enzyme responsible for the conversion of glutamine to glutamate in neurons, as a novel partner of Bmcc1s. Co-immunoprecipitation experiments confirmed that Bmcc1s and KGA form a physiological complex in the brain, whereas binding and modeling studies showed that they interact with each other. Overexpression of Bmcc1s in mouse primary cortical neurons impaired proper mitochondrial targeting of KGA leading to its accumulation within the cytoplasm. Thus, Bmcc1s may control the trafficking of KGA to the mitochondria.