The novel's story is told from the point of view of an unnamed protagonist who happens to find a diary in a hospital one day. The diary belongs to his classmate, a girl named Sakura Yamauchi, who is revealed to be suffering from a terminal illness in her pancreas, and who only has a few months left to live. Sakura explains that the protagonist is the only person apart from her family that knows about her condition. The protagonist promises to keep Sakura's secret. Despite their completely opposite personalities, the protagonist decides to be together with Sakura during her last few months.

Kimi no Suizou wo Tabetai is an adaptation of Sumino Yoru's novel of the same title.

The series was published in English as I Want to Eat Your Pancreas by Seven Seas Entertainment as a 2-in-1 omnibus volume on January 22, 2019. It was also released in Polish by Dango from March 28, 2018, to May 18, 2018; and in Brazilian Portuguese by NewPOP Editora as a 2-in-1 omnibus volume on December 29, 2022.