BCAAs are essential proteogenic amino acids required for protein synthesis and can be utilized for energy production when catabolized. BCAA catabolic rate is mediated through inhibitory phosphorylation of the rate limiting enzyme branched-chain alpha-ketoacid dehydrogenase complex by branched-chain alpha-ketoacid dehydrogenase complex kinase (BCKDK). Pathogenic variants throughout the BCKDK protein structure have been associated with intellectual disability, global developmental delay (motor milestone delay, EEG abnormalities, language impairment), atypically autism, and progressive microcephaly. Patients with loss of function variants had severe depletion of BCAAs, presumably due to increased BCAA catabolism. To test if a previously published Bckdk-/- mouse model had clinically relevant signs of neurodevelopmental delay and postnatal microcephaly with developmental assessments and MicroCT analyses. Our results of these studies implicating increased catabolism of BCAAs, neurodevelopmental delay in Bckdk-/- mice, and postnatal microcephaly. Next, to determine if increased BCAA catabolism is the molecular mechanism of BCKDK deficiency, we measured key BCAA catabolite intermediates of the BCAA pathway and downstream TCA cycle intermediates with LC-MS. Our results implying increased catabolism of BCAAs. After understanding the disease mechanism, two interventions were tested to determine if they could correct disease pathophysiology and biochemical changes in the Bckdk-/- mouse model. These interventions included BCAA repletion and reduced BCAA catabolism through reducing levels of one of the BCKDH subunits, Dbt. BCAA repletion has minimal impact on developmental delay or postnatal microcephaly, although brain size was partially restored. Genetic modulation trended towards correction of these phenotypic changes. Intriguingly genetic modulation of BCAA catabolic rate corrected biochemistry and partially improved neurodevelopmental delay to a larger extent than BCAA repletion, further supporting that the BCAA catabolic rate is the driving cause of metabolic imbalances and the mechanism of action. These findings reveal a novel target to restore biochemical and neurological phenotypes in BCKDK deficiency that should be further explored in controlled, randomized trials. Furthermore, these studies reveal that BCAA catabolism needs to be tightly regulated to maintain normal progression of developmental milestones and homeostasis of brain biochemistry, further solidifying the importance of BCAA metabolism in brain function and neurodevelopment.