After Chicago architect Sam Baldwin loses his wife Maggie to cancer, he and his eight-year-old son Jonah start a new life in Seattle, but they continue to grieve. A year and a half later on Christmas Eve, Jonah calls in to a radio talk show. Jonah persuades a reluctant Sam to go on the air to talk about how much he misses Maggie. Hundreds of women from around the country who hear the program and are touched by the story write to Sam. One of the listeners is Annie Reed, a Baltimore Sun reporter who is engaged to Walter but feels there is something missing from their relationship. After watching the film An Affair to Remember, Annie writes a letter suggesting that Sam meet her on top of the Empire State Building on Valentine’s Day. She decides not to mail it, but her friend and editor Becky does it for her and later agrees to send Annie to Seattle.
Sam begins dating a co-worker, Victoria, whom Jonah dislikes. Jonah reads Annie’s letter and likes that it mentions the Baltimore Orioles, but he fails to convince his father to go to New York to meet Annie. On the advice of his playmate Jessica, Jonah replies to Annie, agreeing to the New York meeting. While dropping Victoria off at the airport for a flight, Sam sees Annie exiting from her plane and is mesmerized by her, although he has no idea who she is. Annie later secretly watches Sam and Jonah playing on the beach together. The next day she goes again to Sam’s houseboat but mistakes Sam’s sister for Victoria. He recognizes her from the airport and says “hello” but Annie only responds with “hello” before leaving. She returns to Baltimore and then goes to New York to meet Walter for Valentine’s Day.
With Jessica’s help, Jonah flies to New York and goes to the Empire State Building searching for Annie. When Sam discovers what Jonah did, he grabs a later plane and follows Jonah where he finds him on the observation deck. Meanwhile, Annie sees the skyscraper from the Rainbow Room where she is dining with Walter and confesses her doubts to him, amicably ending their engagement. She rushes to the Empire State Building and arrives on the observation deck just moments after the doors to the down elevator close with Sam and Jonah inside.
The observation deck is deserted, but Annie discovers the backpack Jonah left behind. As she pulls out Jonah’s teddy bear from the backpack, Sam and Jonah emerge from the elevator having returned to fetch it, and the three meet. After Sam and Annie stare at each other in recognition, Sam says they should go and offers his hand to Annie. The three then enter the elevator together and the doors close.