Here we showed that the type 3 IP₃ receptor (IP₃R3) is specifically expressed in hair follicles of the skin and plays an important role in the regulation of the hair cycle. We found that IP₃R3-deficient (Itpr3^−/−) mice had prominent alopecia, which was characterized by repeated hair loss and regrowth. The alopecic stripe runs along the body axis like a wave, suggesting disturbed hair-cycle regulation. Indeed, the hair follicles of the alopecic region were in the early anagen stage. Although the hair growth and proliferation activity of the hair matrix cells in the anagen phase were normal in Itpr3^−/− mice, telogen club hairs in the telogen–anagen transition phase were loosely attached to the hair follicles and were easily removed in contrast to the more tightly attached club hairs of Itpr3^+/+ mice. Itpr3^−/− keratinocytes surrounding the telogen club hairs have sparse cytokeratin filaments extending in random directions, as well as less developed desmosomes. Furthermore, nuclear factor of activated T cells c1 (NFATc1) failed to translocate into the nucleus of keratin 6–positive bulge cells in Itpr3^−/− telogen follicles. We propose that hair shedding is actively controlled by the IP₃R3/NFAT-dependent signaling pathway, possibly through the regulation of cytokeratin filaments in keratinocytes.