Recent investigations have demonstrated that melatonin influences carbohydrate metabolism mediated by insulin-inhibiting effects on pancreatic β-cells. This study evaluated whether melatonin has also an effect on pancreatic α-cells and glucagon expression as well as the glucagon secretion in vitro and in vivo. Glucagon-producing pancreatic α-cell line αTC1 clone 9 (αTC1.9) was used, which was characterized as an appropriate model with glucose responsiveness and expression of the melatonin receptors MT1 and MT2. The results demonstrate that melatonin incubation significantly enhanced the expression as well as the secretion of glucagon. These effects appeared to be more pronounced under hyperglycemic conditions compared to basal glucose concentrations. Notably, in vivo studies demonstrated that long-term oral melatonin administration led to significantly elevated plasma glucagon concentrations in Wistar rats. In contrast, plasma glucagon levels were found to be slightly decreased in type 2 diabetic Goto-Kakizaki rats. Moreover, investigations measuring the relative glucagon receptor mRNA expression showed marked differences in the liver of melatonin-substituted rats as well as in melatonin receptor knockout mice. In conclusion, these findings revealed evidence that melatonin influences pancreatic glucagon expression and secretion as well as the peripheral glucagon action.