Born in Wakayama, Japan, he graduated from the Osaka School of Design in 1979 and a couple years later joined the studio Annapuru as an animator for the TV series Tomorrow's Joe. While working there, he saw some animation by Takashi Nakamura in Gold Lightan, an otherwise standard mecha TV series by a rival studio. He was impressed, and it inspired him to quit his job and become a freelance animator.
Morimoto often collaborated with Nakamura, most notably in Katsuhiro Otomo’s "The Order to Stop Construction" segment of the anthology film Neo-Tokyo. This opened many doors for him, from working as animation director on Otomo's landmark feature Akira and a chance to direct a short for the Robot Carnival anthology. Around this time he founded Studio 4°C with producer Eiko Tanaka and fellow animator Yoshiharu Sato.
Since then, Morimoto has focused almost exclusively on his directing work. His work became increasingly unusual with time. This is best represented by the concert scenes in Macross Plus and his short film Noiseman Sound Insect.
Aside from a small cult following, his films have been ignored outside of Japan. This has begun to change in recent years, with his artwork being featured in Takashi Murakami's Superflat exhibitions worldwide, and being invited by the Wachowski Brothers to direct "Beyond", a segment of The Animatrix. He is currently working on Sachiko, his second feature-length film.