Pancreatic α‐cells secrete glucagon to maintain energy homeostasis. Although histamine has an important role in energy homeostasis, the expression and function of histamine receptors in pancreatic α‐cells remains unknown. We found that the histamine H3 receptor (H3R) was expressed in mouse pancreatic α‐cells and αTC1.6 cells, a mouse pancreatic α‐cell line. H3R inhibited glucagon secretion from αTC1.6 cells by inhibiting an increase in intracellular Ca2+ concentration. We also found that immepip, a selective H3R agonist, decreased serum glucagon concentration in rats. These results suggest that H3R modulates glucagon secretion from pancreatic α‐cells.