Glutaric aciduria (GA1) and pyridoxine-dependent epilepsy (PDE) are two inherited disorders caused by enzymatic defects in the lysine catabolism pathway. Both are characterized by the accumulation of toxic metabolites in the central nervous system. Currently, the available treatment consists on dietary restriction of lysine complemented with carnitine in GA1 or pyridoxine in PDE. Unfortunately, neither treatment fully prevents the neurological injury. In this study we propose a gene therapy strategy consisting in the silencing of the first enzyme of the lysine degradation pathway, the alpha-aminoadipic semialdehyde synthase (AASS), as a common therapeutic approach for GA1 and PDE. We developed an interfering RNA (iRNA)-based therapeutics using adeno-associated viruses (AAV) targeting AASS transcripts (AAV-iAASS). Ex vivo validation in human and mouse cell lines showed a reduction of AASS protein expression and enzymatic activity, slowing down the catabolism of lysine. In vivo assays in GA1 mouse models receiving AAV-iAASS, showed good AAV biodistribution and AASS inhibition in striatum, the main brain structure affected in GA1. Results on the functional impact of this therapy rescued the accumulation of neurotoxic metabolites. Lysine overload triggered a very severe phenotype in GA1 mice compromising the survival in 50% of animals. Interestingly, animals treated with AAV-iAASS gained weight and improved survival. Our results suggest that AAV-iRNA against AASS is an attractive therapeutic strategy for GA1 and PDE.