Calcineurin is a Ca2+/calmodulin‐dependent protein phosphatase consisting of two subunits – catalytic subunit A (CnA) and regulatory subunit B (CnB) – and plays a critical role in transducing Ca2+ signals into cellular responses. In this study, we investigated the expression of calcineurin in the mouse developing tooth. In‐situ hybridization detected mRNAs for the CnAα and CnAβ isoforms of CnA and for the CnB1 isoform of CnB in the upper molar tooth germ at embryonic day 15. Immunohistochemistry with antibodies specific for CnAα, CnAβ, and CnB1 showed strong immunoreactivity of these proteins in secretory‐stage ameloblasts and in odontoblasts during dentin formation. CnAβ and CnB1 were strongly immunoreactive in ruffle‐ended ameloblasts at the enamel‐maturation stage. In ameloblasts and odontoblasts, we also noted different subcellular distributions of CnAα and CnAβ. From these data, temporal profiles of calcineurin expression appear to correlate with active mineralization in tooth development. Furthermore, the distinct subcellular distribution of the two CnA subunits may reflect their distinct substrates or responsive sites within single cells, thus contributing to the diversity of calcineurin‐dependent cellular responses during active tooth mineralization.