Shizuku Tsukishima is a junior high school student, living in a cramped apartment with her father, mother, and sister. As she returns from an errand to the store, her father who is a librarian, mentions how they're converting their check-out system, so that the check-out cards at the front of the books will now become obsolete. Pondering this, Shizuku goes to read a book that she checked out, and is drawn to the name Seiji Amasawa on the card. Checking her other library books, she's amazed to see that his name also appears on their cards as well!
The next day, Shizuku gets up and goes early to school. Shizuku gets one of her teachers to allow her to check a book out from the school library, since the local public library does not have a copy. Looking over the book, she notices a dedication inside, that mentions the name Amasawa. While she is pondering this, her friend Yuko appears, and the two go off to talk.
Shizuku has been working on a translation of the American song, "Take Me Home, Country Roads." While Yuko likes it, Shizuku still feels it's 'trite.' She also reveals a parody she wrote titled 'Concrete Roads,' the lyrics of which amuse them both. After a little bit, Yuko becomes serious, and secretly reveals that she got a love letter, but her feelings are torn, as she actually likes someone that she and Shizuku know: a boy named Sugimura.
Shizuku then accompanies Yuko to her cram school lessons (important high-school entrance exams are a short time away), but then realizes that she left the book she checked out back at school. Going back to where she was sitting, she finds a boy there, reading it. He mentions her name (which he found in the check-out card on the front), and makes a mention that 'Concrete Roads' needs some work. This infuriates Shizuku, who stews over this critique of her writing all the way home. Later on that day, her older sister returns from visiting relatives, and begins critiquing Shizuku even more, much to her consternation.
The next day, Shizuku plans to go to the library where her father works. Her sister makes a lunch for her to deliver to him as well. Getting on the train, Shizuku is surprised to see a large cat board the train. Curiously, she follows it out and into the city. After some time, the cat leads her to a small shop in a quiet neighborhood. Entering the shop, she is greeted by its owner, an old man named Shiro Nishi. Seeing her admiring a statue of a humanized cat in a suit, he then shows her a grandfather clock he has been restoring. However, realizing how late it is, Shizuku runs off to the library, but overjoyed at the wonderful little shop. Upon reaching the library, she suddenly realizes she left her father's lunch at the store. However, the boy she met previously who 'critiqued' her work appears, and gives it to her. He makes a little joke about the lunch being pretty big for her, and leaves singing 'Concrete Roads.' This just infuriates Shizuku even more with the mysterious boy.
After some time, school finally starts up for Shizuku. During a break period while talking with Yuko, Sugimura appears, and Shizuku (knowing of Yuko's crush) hints that the two should study together. Yuko grows upset and drags Shizuku away, chastising her friend for her 'playful help.'
Still curious about the dedication in the book she checked out, Shizuku goes to the teacher's lounge, where someone informs her that a Mr. Amasawa donated it, and that he also has a son who goes to the school. Shizuku bolts from the room, feeling that somehow, the boy she saw is Mr. Amasawa's son. While heading to lunch, she and Yuko pass by the boy again, who passes without a word. For some reason, this seems to upset Shizuku.
At lunch, Yuko regales two of their classmates and a teacher with this news, and the girls tease Shizuku that 'springtime has finally come for her.' Shizuku vehemently denies any feelings for the boy, and holds back showing the latest work on her translation of "Take Me Home, Country Roads" unless the girls apologize. Doing so, they read the new translation, and admit to really liking the newly translated lyrics.
On her way home from school, Shizuku stops by the little shop, only to find it closed. Later that night, she gets a call from Yuko, whom she meets at a nearby park. Yuko is in tears after she met with Sugimura, who was relaying a message from another boy about asking her out. The fact that it was Sugimura who made this requests upsets her so much, that she decides not to go to school the next day.
The next day at school, Sugimura meets up with Shizuku, and they discuss what happened. Sugimura is not sure what he did to make Yuko run off and cry. Shizuku chastises him for not understanding that Yuko has feelings for him. The surprise on Sugimura's face is soon reflected in Shizuku's, when he reveals that he actually likes her! Shizuku rejects this idea, saying she just wants to be friends with him. Later on that evening, Shizuku sobs about how 'dense' she is about love as well.
Later on, she gets on the train and goes back to the little shop. Still closed, she notices the cat, who sits down next to her. She begins to talk to it to get her mind off things. As she does so, the boy she saw the other day appears, and begins to have a conversation with her. He notes to her that he knows the cat, and calls him Moon ("Because he looks like a full moon"). However, the cat has no actual owner, and he's heard other people have their own names for him. The boy then reveals that his Grandfather owns the little shop, but that he's away at the moment. However, he allows Shizuku to enter the shop from the rear entrance.
Bringing her onto the main floor, Shizuku is surprised to see the Grandfather clock is gone. The boy explains that his Grandfather had just completed fixing it the day she forgot her lunch. Still upset over that joke, Shizuku is then surprised when the boy shows her the cat statue, which the boy dubs 'The Baron.' A cleaning accident to the statue, resulted in the eyes on the statue sparkling brilliantly in the setting sun from the nearby window.
Afterwards, the boy shows Shizuku a workshop in the basement, where violin-making lessons are taught. He reveals that he wants to make this his profession, but admits that he still isn't that good at it. Overjoyed at such a creative venture, Shizuku asks him if he can play a violin. When he affirms this, she begs for him to play for her. He agrees on the condition that she sing. He begins to play "Take Me Home, Country Roads," and Shizuku begins to sing her translation. As she does, Grandfather and some of his friends come home, and join in with their own instruments. At the end of the song, they are all introduced, and Shizuku finds out the name of the boy: Seiji Amasawa. The same Seiji that had been checking out the same books as her.
Later on that night, Seiji walks her partway home, as they discuss his plans to go to Cremona, Italy, where he wants to study violin-making. Grandfather is all for it, but Seiji's Father is against it. As Shizuku takes leave, Seiji mentions that he actually did like her song parody, "Concrete Roads." This leaves Shizuku in a good mood as she heads home.
The next day, Shizuku sees that Yuko is back in school, but a rumor has circulated that someone saw Shizuku walking with a boy. Shortly afterward, Sugimura appears to chat with Yuko, telling her that he will tell his friend (whom he relayed the message from the other day) that she turned down his request. As Sugimura leaves, Yuko smiles in a relieved fashion. When Seiji comes by the room asking to see Shizuku, the classroom erupts into a raucous cheer that Shizuku (finally) has a boyfriend! Shizuku angrily storms off, and takes Seiji to the roof where they can talk.
Seiji informs her that his Father will allow him to go to Italy, and the two have an intimate conversation, where Shizuku reveals that she seems to be developing feelings for him. However, some of her classmates have been spying on them, and she chases them off. For the rest of the day, she is very quiet, deep in thought.
Later on that evening, she goes to Yuko's house to talk to her. Shizuku feels distraught for a number of reasons. One is that if Seiji goes to Italy, he'll be gone for several years, and she won't see him for quite some time. Another reason is that she feels that Seiji is working towards accomplishing a goal...something she doesn't have. Yuko points out that Shizuku does have talent, given how well she translated the song "Take Me Home, Country Roads." Yuko's observation energizes Shizuku, who vows to write a story. On her way home, she happens to see Moon leaving a person's house, and a little girl in the doorway calls him 'Muta.'
Shizuku then begins to write her story, and consults with Seiji's Grandfather, who applauds her determination. On one visit, he shows her a rock that had been chipped away, revealing some lapis lazuli inside. This helps to inspire Shizuku even more in her writing, as she uses the lapis lazuli and the statue of the Cat Baron for inspiration. Sometime afterward, she meets up with Seiji again, who is going off to Italy. They say their goodbyes, and Shizuku continues to work on her story.
However, her determination soon begins to get in the way of other things, such as her schoolwork. After her Mother is called to the school, and her sister sees the grades from a 'mock quiz,' Shizuku's Father sits down with her to talk. Shizuku reveals that she does care about her studies, but also needs to do what she is doing to better herself. Her Father shows sympathy, and allows her to continue what she is doing.
Finally, Shizuku finishes the story, titled 'Whisper of the Heart.' She goes to Seiji's Grandfather, requesting he read it and let her know how she did. Once he finishes it, she panics, admitting that it is not perfect. However, he admits while it was not perfect, she can still keep refining it. The wave of exhaustion and realizing that it is not perfect, causes her to break down in tears, as she admits that she feels so far behind Seiji in achieving something. Seiji's Grandfather realizes how much she cares for his Grandson, and treats her to dinner to calm her down.
After dinner, Seiji's Grandfather tells Shizuku that her story had some interesting points, notably that the Baron had a wife. In real life, the Cat Baron statue did have a partner. He had found the two statues while living in Europe, but the Baron's wife was being fixed at the time. It was then that Seiji's Grandfather decided that he would take the Baron statue, and his girlfriend would join him later, bringing the Baron's wife. However, this was during the war, and he never saw her or the Baron's wife again. Before Shizuku leaves, she is given the chipped rock with the lapis lazuli center as a gift.
Very early the next morning, Shizuku awakes to find Seiji waiting outside! She rushes down to see him, and gets on his bicycle, as he peddles her towards a hidden place. When they arrive on a hillside, they are just in time to see the sun rise over the hills. It is then that Seiji reveals his true feelings, and that he is willing to wait for Shizuku, if she will wait for him. She agrees, and he embraces her, declaring his love for her.