A manufacturing method of a vertical GaN-based semiconductor device having: a GaN-based semiconductor substrate; a GaN-based semiconductor layer including a drift region having doping concentration of an n type impurity, which is lower than that of the GaN-based semiconductor substrate, and is provided on the GaN-based semiconductor substrate; and MIS structure having the GaN-based semiconductor layer, an insulating film contacting the GaN-based semiconductor layer, and a conductive portion contacting the insulating film, the method includes: implanting an n type dopant in a back surface of the GaN-based semiconductor substrate after forming of the MIS structure, and annealing the GaN-based semiconductor substrate after the implanting of the n type dopant.