Fujimoto is a character in Ponyo on the Cliff by the Sea. He's described as being less of a villain than a father who ends up pushing his daughter away the more he tries to protect her, which Miyazaki believed to be a trend in many Japanese fathers in this day and age. Although he was once a human, he became disenchanted with his people's disrespectful disregard for the environment and the life it cultivates, and decided to live in the sea, building an underwater fortress for himself and forsaking his humanity. As a result, he is forced to take a back-mounted machine with him whenever he ventures onto dry land, as it carries a vat of salt water that he must spray around himself, though the exact reasons why he must do this are never stated; perhaps his feet can't touch the ground, or perhaps magic figures into it. His other main invention is a large submarine-like vehicle that serves as his main mode of transportation.

At some point around his leaving the human world he fell in love with the minor sea goddess Granmammare; it is possible that she was his reason for leaving his human world. During that time he and Granmammare married, she bore him Ponyo, whom he calls by her birthname "Brunhilde," and many other (possibly hundreds) of daughters like Ponyo. However its obvious that Ponyo doesn't care for her real name. Fujimoto is known for unsuccessfully trying to shelter her. Ponyo seems to be the oldest of their children and has thus inherited more of his magic along with Granmammare's, while their other daughters have only a small amount of magic. They are obviously not as strong as their sister, but do assist in helping Ponyo spend time with Sōsuke, much to Fujimoto's annoyance. Fujimoto's a bit jittery, tending to overreact and also lose his temper at times. Deep down, he does love his daughters and worries for their safety. Once within Granmammmare's presence and calm touch, however, he calms down.

Fujimoto seems to wield significant magical ability, commanding a consummate knowledge of apothecary and an army of violent blobby creatures who answer to his every whim. Additionally, he seems to have a great affinity with much of the life under the sea. Despite this, he takes great pains to keep them away from a gem in his innermost vault, which he intends on using to purge the earth of the taint of humans. In the end, however, thanks to the genuineness of Ponyo's endeavours, he largely reverses his opinion of them, accepting them as basically good in spite of occasional misdeeds.