Pyridoxine-dependent epilepsy (PDE), a rare autosomal recessively inherited metabolic disease, results from mutations in ALDH7A1, a gene crucial for lysine metabolism. Although early high-dose pyridoxine treatment can control seizures, ∼75% of PDE patients still have intellectual disabilities. In this study, we test the hypothesis of substrate reduction therapy for PDE by genetically perturbing lysine α-ketoglutarate reductase (LKR), an enzyme upstream of the defective ALDH7A1, in male and female laboratory mice. A homozygous mutation in LKR completely abolishes the accumulation of toxic lysine catabolism intermediates (α-aminoadipic-δ-semialdehyde and its cyclic form, δ-1-piperideine-6-carboxylate), ends the epileptic state, and restores the defective brain development and cognitive impairments in ALDH7A1-deficient mice. Therefore, these genetic data prove the concept of the effectiveness of substrate reduction therapy for PDE via LKR inhibition.