When Marnie was there follows Anna Sasaki staying with her relatives in a town in Kushiro wetlands, Hokkaido. Anna comes across a nearby abandoned mansion, where she meets Marnie, a mysterious girl who asks her to promise to keep their secrets from everyone. As summer progresses, Anna spends more time with Marnie and learns the truth about her family and foster care.
The film featured the final work for Studio Ghibli animator Makiko Futaki, who died in May 2016. It was also the final film that Yonebayashi directed for Ghibli before he left and joined Studio Ponoc.