Shizuku Tsukishima is a 14-year-old girl who attends Mukaihara Junior High School, where she is best friends with Yūko Harada. She lives in a Tokyo suburb with her parents Asako, Seiya and older sister Shiho, and is keen on books. One summer evening, she looks through the checkout cards in her library books and discovers they were all checked out previously by someone named Seiji Amasawa.
Shizuku meets Yūko at the school and reveals her rendering of "Take Me Home, Country Roads" she was working on for the school graduation, including a mockery named "Concrete Roads". Yūko reveals that she has a crush on a boy named Sugimura, who happens to be Shizuku's friend. Yūko and Shizuku walk home when she realizes she left her book at the school. She runs back to discover a boy reading her book while teasing her rendering of "Concrete Roads", a set of original lyrics describing Tama New Town that Shizuku based on the song "Take Me Home, Country Roads". The boy tells her how "corny" her lyrics are, which leaves her feeling irritable for the rest of the evening. On the next day, while on her way to the library, Shizuku encounters a cat commuting on the train, and follows it to discover an antique shop run by Shirō Nishi. In the shop there is a cat statuette nicknamed The Baron as well as a centuries old antique clock. Realizing she's late for the library, Shizuku runs out feeling ecstatic about finding "a place where stories begin", only to run into the boy she had met the previous day, who returns the lunchbox she left behind. He comments on how much food is in the box and rides away, singing her song, leaving Shizuku in another foul mood.
When school restarts, Yūko is devastated when Sugimura asks her to reply to a love letter his teammate sent. Shizuku confronts Sugimura and scolds him for his actions, only for him to reveal he had a crush on her. However, she rejects him in order to not hurt Yūko. Shizuku leaves feeling leveled. Feeling disconsolate, Shizuku decides to head to the antique shop, meeting the boy once more. He shows her the workshop, where she discovers that he is learning to make violins to pursue his dream of becoming a master luthier. She begs him to play the violin for her, but he agrees on the condition that she sings along. The pair perform "Take Me Home, Country Roads". The boy is revealed to be Seiji, Nishi's grandson, and Shizuku and Seiji finally befriend each other.
Seiji admits that he admires Shizuku’s talents, and reveals his dream to become a luthier, as well as his efforts of checking out a large number of books in the hopes that she would eventually notice him. Days after, Seiji leaves for Cremona, Italy for a two-month study with a master violin-maker. Inspired by Seiji, Shizuku decides to pursue her skill for writing seriously in the same two months. She asks Nishi if she can write a story featuring the Baron, to which Nishi grants his consent in exchange for being the first to read her story.
Shizuku concocts a fantasy story featuring herself as the protagonist, the Baron as the male hero looking for his lost love, Louise, and the cat from the train (a neighborhood stray who is, among other names, known as "Moon" and "Muta") as the antagonist. Devoting her time to her writing, Shizuku stays up until early in the morning, and her school grades drop. She argues with her family over her grades and future. As she continues to push herself, her anxiety mounts.
When her story is complete, Nishi reads it and gives his honest assessment. Shizuku bursts into tears as the stress of the last two months turns into relief. Nishi consoles her and tells her the real-life story of the Baron. When he studied in Germany in his youth, he found his first love, a woman named Louise. Nishi discovered the twin statuettes of the Baron and his female companion in a cafe, but as the female one was away for repairs, the shopkeeper would only allow Nishi to buy the Baron if Louise agreed to hold onto its companion so they could be reunited. However, the two lovers and their cat statues were separated during World War II. In the original Japanese script, Shizuku never knew of the truth of the Baron's origin or of Louise, and Seiji earlier tells her that his grandfather refuses to speak of it. This makes Shizuku's inclusion of Louise in the story a tremendous coincidence, or something else. In the English dub, Seiji's dialogue is changed and he briefly tells her about Louise.
Deciding she needs to learn more about writing, and that she wants to attend high school, Shizuku announces to her mother that she will resume studying for her high school entrance exams. Shizuku wakes up early in the morning and sees Seiji outside on his bicycle, having returned a day earlier. In the English dub, Seiji tells Shizuku he decided to finish high school before returning to Cremona to become a luthier, differing from the Japanese dialogue, in which he says he will return to Cremona after middle school graduation as planned.
Seiji takes Shizuku on his bike to a hidden lookout, where they see the sunrise. Seiji professes his love for Shizuku and proposes that they marry in the future; she happily accepts.
Shizuku's "Take Me Home, Country Roads" plays over the ending credits while daily life in her hometown is observed body.