Sam Baldwin, a Chicago architect, has lost his wife (Carey Lowell) to cancer. He and his young son Jonah move to Seattle, Washington to make a fresh start, but Sam is still disconsolate. On Christmas Eve, Jonah calls into a national radio advice show and persuades his father to go on the air with him to talk about how much he misses his wife. Thousands of women around the country, touched by Sam's story, send him letters. One letter is from Annie Reed, a journalist from Baltimore, Maryland, engaged to a nice but sneeze-prone man named Walter (Bill Pullman), who feels that there is something missing.
Meanwhile, Jonah, who has been working his way through the flood of mail, finds Annie's missive and likes that it mentions the Baltimore Orioles. He tries to convince his father to go to New York City to meet her on Valentine's Day, but Sam loses his temper and refuses. Sam begins to see a coworker, Victoria, whom Jonah cannot bear because, among other things, she "acts like a ho" and "laughs like a hyena". On the advice of a friend, Jonah mails a letter to Annie agreeing to meet at the top of the Empire State Building on Valentine's Day. At the airport, while dropping Victoria off for a flight, Sam sees Annie getting off the plane and is momentarily entranced.
Annie, on a whim, has traveled to Seattle to meet Sam. She watches him and Jonah playing on the beach together, and on the advice of a friend, Becky, she decides to meet and talk to him. Next day, she sees Sam with his sister Suzy, and thinking she is his girlfriend, stops in the middle of the street. Sam recognizes her, and says hello; all she can respond is hello back, a reference to the movie An Affair to Remember, which she later tells Becky about. Annie then decides she has been being silly and nervous, and goes to New York to meet Walter.
Jonah flies to New York and takes a taxi to the Empire State Building, saying he's going to meet his new mother. Sam, in pursuit, catches up with Jonah, who hasn't found Annie. Meanwhile Annie sees the Empire State Building from the restaurant at which she is eating, and breaks up with her fiancé. Jonah and Sam get on the down elevator just before Annie reaches the top of the building. There she finds Jonah's backpack with a teddy bear in it, not knowing who it belongs to. Jonah and Sam come back to the top to find the backpack, where they meet Annie for the first time.
