NBCe1 (electrogenic Na⁺/HCO₃^– cotransporter 1) is a product of gene SLC4A4 and has five splice variants, NBCe1-A through NBCe1-E. In agreement with an essential role of NBCe1 in cellular pH regulation, human families carrying missense mutations of gene SLC4A4 show proximal renal tubular acidosis. Some of them exhibit brain function-related symptoms, such as migraine and mental retardation, but physiological roles of NBCe1 in brain function remain unclear. To gain insights into NBCe1-specific functions in the brain, we herein identified proteins that specifically bind to a unique C-terminal region of NBCe1-C, a brain-specific NBCe1 isoform. We found that a catalytic subunit of calcineurin binds to the C terminus of NBCe1-C in the mouse cerebellum. Heterologous-coexpression experiments revealed that calcineurin binds to NBCe1-C via a “PQIRIE” motif at its C terminus. The interaction enhanced cell surface expression of NBCe1-C, resulting in an increase of its transporter activity, for which the phosphatase activity of calcineurin was essential. When NBCe1-C was stably expressed in HeLa cells, its cell surface expression was enhanced by an intracellular Ca²⁺ concentration increase and was suppressed by FK506, a specific inhibitor of calcineurin. These mechanisms of surface expression and transport activity of NBCe1-C regulated by the Ca²⁺–calcineurin axis indicate specialized functions of NBCe1-C in the brain.