After graduating from high school, Kubota went through training at Toei Animation's research center before dropping out and joining Xebec in 1998. Three years later in he met Sushio at Comiket, which led to Kubota joining Gainax. There he made his debut as an animation director on the premiere of Mahoromatic's second season.
In 2005, he made his debut as a character designer, although still jointly together with Sushio and Takaaki Yamashita, on the 6th One Piece movie. The film was directed by Mamoru Hosoda, which led to Kubota getting an invite to join the production of The Girl Who Leapt Through Time as an animation director. After this he kept working at Gainax until going freelance.
In 2012, he worked as the main character designer on From the New World and Robotics;Notes, and a few years later he served as one on One-Punch Man, which earned him international fame.
