The 36-year-old driver was arrested late Wednesday after his vehicle hit the boy who was crossing a street in the city of Ichinomiya, Aichi prefecture, local police said.
"I did not keep my eyes to the front as I was playing the Pokemon Go game while driving," the man told police.
It was the second fatal accident in Aichi prefecture linked to the augmented-reality mobile game since its release in Japan in July, local police said.
The game, in which computer-generated Pokemon characters are superimposed onto real locations, has been a sensation this year with over 100 million downloads worldwide and an estimated daily revenue of 10 million dollars.