Leigh syndrome (LS) is the most common infantile mitochondrial encephalopathy. No treatment is currently available for this condition. Mice lacking $Ndufs4$, encoding NADH: ubiquinone oxidoreductase iron-sulfur protein 4 recapitulates the main findings of complex I related LS, including severe multisystemic complex I deficiency and progressive neurodegeneration. In order to develop a gene therapy approach for LS, we used here an AAV2/9 vector carrying the human $NDUFS4$ coding sequence (hNDUFS4). We administered AAV2/9-$hNDUFS4$ by intravenous (IV) and/or intracerebroventricular (ICV) routes to either newborn or young $Ndufs4$$\mathrm{<mrow\; data-mjx-texclass="ORD">-<mrow\; data-mjx-texclass="ORD">/</mrow>-</mrow>}$ mice. We found that IV administration alone was only able to correct the complex I deficiency in peripheral organs, while ICV administration partially corrected the deficiency in the brain. However, both treatments failed to improve the clinical phenotype or to prolong the lifespan of $Ndufs4$$\mathrm{<mrow\; data-mjx-texclass="ORD">-<mrow\; data-mjx-texclass="ORD">/</mrow>-</mrow>}$ mice. In contrast, combined IV and ICV treatments resulted, along with increased complex I activity, in the amelioration of the rotarod performance, and in a significant prolongation of the lifespan. Our results indicate that extraneurological organs play an important role in LS pathogenesis, and provide an insight into current limitations of AAV-mediated gene therapy in multisystem disorders. These findings warrant future investigations to develop new vectors able to efficiently target multiple organs.