Autophagy is a lysosomal degradation pathway important for cellular homeostasis and survival. Inhibition of the mammalian target of rapamycin (mTOR) is the best known trigger for autophagy stimulation. In addition, intracellular Ca²⁺ regulates autophagy, but its exact role remains ambiguous. Here, we report that the mTOR inhibitor rapamycin, while enhancing autophagy, also remodeled the intracellular Ca²⁺-signaling machinery. These alterations include a) an increase in the endoplasmic-reticulum (ER) Ca²⁺-store content, b) a decrease in the ER Ca²⁺-leak rate, and c) an increased Ca²⁺ release through the inositol 1,4,5-trisphosphate receptors (IP₃Rs), the main ER-resident Ca²⁺-release channels. Importantly, buffering cytosolic Ca²⁺ with BAPTA impeded rapamycin-induced autophagy. These results reveal intracellular Ca²⁺ signaling as a crucial component in the canonical mTOR-dependent autophagy pathway.