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Inactivating mutations in the PPT1 gene encoding palmitoyl‐protein thioesterase‐1 (PPT1) underlie the CLN1 disease, a devastating neurodegenerative lysosomal storage disorder. The mechanism of pathogenesis underlying CLN1 disease has remained elusive. PPT1 is a lysosomal enzyme, which catalyzes the removal of palmitate from S‐palmitoylated proteins (constituents of ceroid lipofuscin) facilitating their degradation and clearance by lysosomal hydrolases. Thus, it has been proposed that Ppt1‐deficiency leads to lysosomal accumulation of ceroid lipofuscin leading to CLN1 disease. While S‐palmitoylation is catalyzed by palmitoyl acyltransferases (called ZDHHCs), palmitoyl‐protein thioesterases (PPTs) depalmitoylate these proteins. We sought to determine the mechanism by which Ppt1‐deficiency may impair lysosomal degradative function leading to infantile neuronal ceroid lipofuscinosis pathogenesis. Here, we report that in Ppt1−/− mice, which mimic CLN1 disease, low level of inositol 3‐phosphate receptor‐1 (IP3R1) that mediates Ca++ transport from the endoplasmic reticulum to the lysosome dysregulated lysosomal Ca++ homeostasis. Intriguingly, the transcription factor nuclear factor of activated T‐cells, cytoplasmic 4 (NFATC4), which regulates IP3R1‐expression, required S‐palmitoylation for trafficking from the cytoplasm to the nucleus. We identified two palmitoyl acyltransferases, ZDHHC4 and ZDHHC8, which catalyzed S‐palmitoylation of NFATC4. Notably, in Ppt1−/− mice, reduced ZDHHC4 and ZDHHC8 levels markedly lowered S‐palmitoylated NFATC4 (active) in the nucleus, which inhibited IP3R1‐expression, thereby dysregulating lysosomal Ca++ homeostasis. Consequently, Ca++‐dependent lysosomal enzyme activities were markedly suppressed. Impaired lysosomal degradative function impaired autophagy, which caused lysosomal storage of undigested cargo. Importantly, IP3R1‐overexpression in Ppt1−/− mouse fibroblasts ameliorated this defect. Our results reveal a previously unrecognized role of Ppt1 in regulating lysosomal Ca++ homeostasis and suggest that this defect contributes to pathogenesis of CLN1 disease. [ABSTRACT FROM AUTHOR]