Infantile neuronal ceroid lipofuscinosis (INCL) is a severe neurodegenerative disease caused by deficiency of palmitoyl protein thioesterase 1 (PPT1). INCL results in dramatic loss of thalamocortical neurons, but the disease mechanism has remained elusive. In the present work we describe the first interaction partner of PPT1, the F₁-complex of the mitochondrial ATP synthase, by co-purification and in vitro-binding assays. In addition to mitochondria, subunits of F₁-complex have been reported to localize in the plasma membrane, and to be capable of acting as receptors for various ligands such as apolipoprotein A-1. We verified here the plasma membrane localization of F₁-subunits on mouse primary neurons and fibroblasts by cell surface biotinylation and TIRF-microscopy. To gain further insight into the Ppt1-mediated properties of the F₁-complex, we utilized the Ppt1-deficient Ppt1^Δex4 mice. While no changes in the mitochondrial function could be detected in the brain of the Ppt1^Δex4 mice, the levels of F₁-subunits α and β on the plasma membrane were specifically increased in the Ppt1^Δex4 neurons. Significant changes were also detected in the apolipoprotein A-I uptake by the Ppt1^Δex4 neurons and the serum lipid composition in the Ppt1^Δex4 mice. These data indicate neuron-specific changes for F₁-complex in the Ppt1-deficient cells and give clues for a possible link between lipid metabolism and neurodegeneration in INCL.