Makoto Shinkai was born Makoto Niitsu on February 9, 1973, and his hometown is Nagano, Japan. He studied Japanese literature as a university student. In interviews, Shinkai has stated that he traces his passion for creation to the manga and anime he had exposure to as a middle school student. Shinkai has also been quoted as saying that Hayao Miyazaki's Castle in the Sky is his favorite anime.

Shinkai started out as a graphic designer for a video game company called Falcom. In 1999, Shinkai released his five-minute monochromatic animated short, "She and Her Cat." Shinkai provided the voice for the cat, and his fiancee, Mika Shinohara, provided the voice for the cat's owner. The short ended up winning several awards, including the grand prize at the 2000 DoGA Animation contest.

Shinkai has another early work called Other Worlds, which he animated and directed. This black and white piece is under two minutes in length, and it features a man and a woman talking about their relationship.

In June 2000, Shinkai drew a picture of a girl in a cockpit holding a cell phone. This picture became the inspiration for his next work, Voices of a Distant Star. Later, Mangazoo contacted Shinkai and gave him a grant to turn Voices of a Distant Star into an anime they could sell. In May 2001, Shinkai quit his job at Falcom, and began working on Voices of a Distant Star. Shinkai provided a voice in the original cut of the project, but his voice was replaced in the final product. Shinkai's fiancee provided the voice for Mikako, the main female character in Voices of a Distant Star, in the original cut of the project. This OVA was released on February 2, 2002.

In 2003, Shinkai directed an anime music video for a song called "Egao," which features a girl and her pet hamster. In 2004, Shinkai did some CG work on Wind: A Breath of Heart.

Shinkai's next major project was the feature-length film, The Place Promised in Our Early Days. The film was released to Japanese theaters on November 20, 2004. This was followed by 5 Centimeters per Second, which was released on March 3, 2007. Also in 2007, Shinkai directed a promotional piece for Neko no Shukai. He also wrote, directed, and produced the 2011 anime film, Children Who Chase Lost Voices.

Besides the work he is best known for, Shinkai has also done animation for commercials, and he assists in animating visual novel opening movies for a company called Minori.