It is generally accepted that voltage-gated Ca²⁺ channels, CaV, regulate Ca²⁺ homeostasis in excitable cells following plasma membrane depolarization. Here, we show that the Ca²⁺ protein α1D of CaV1.3 channel is overexpressed in colorectal cancer biopsies compared to normal tissues. Gene silencing experiments targeting α1D reduced the migration and the basal cytosolic Ca²⁺ concentration of HCT116 colon cancer cell line and modified the cytosolic Ca²⁺ oscillations induced by the sodium/calcium exchanger NCX1/3 working in its reverse mode. Interestingly, NCX1/3 regulated membrane potential of HCT116 cells only when α1D was silenced, and blocking NCX1/3 increased cytosolic Ca²⁺ concentration and cell migration. However, membrane depolarization did not induce an increase in intracellular Ca²⁺. Patch-clamp experiments clearly showed that the inward Ca²⁺ current was absent. Finally, flow cytometry and immunofluorescence studies showed that α1D protein was localized at the plasma membrane, in cytosol and cell nuclei. Altogether, we uncover a novel signaling pathway showing that α1D is involved in the regulation of Ca²⁺ homeostasis and cell migration by a mechanism independent of its plasma membrane canonical function but that involved plasma membrane Na⁺/Ca²⁺ exchanger.