In 1933 in New York City, eleven-year-old Annie sleeps in an orphanage with several other girls her age. When six-year-old Molly wakes up from a bad dream, Annie comforts her by singing about her own parents; even though they abandoned her at the orphanage as a baby, she holds on to the hope that they will come back for her ("Maybe"). Annie decides to escape to find her parents, but is caught by Miss Hannigan, the cruel keeper of the orphanage. To punish Annie's behavior, she forces all the girls to clean, and they lament the terrible conditions of the orphanage ("It's the Hard Knock Life"). Later on, Bundles the laundry man comes in to pick up the blankets, allowing Annie to escape in his truck. Miss Hannigan realizes she's gone and chases after the truck. The other orphans cheer her on, but await punishment when Hannigan returns ("Hard Knock Life (Reprise)").
Annie escapes, running into a friendly stray dog. She tells him of better days to come ("Tomorrow"). She fools a police officer into believing he is her dog, named Sandy. Later, Annie and Sandy stumble upon a Hooverville, a shanty town full of formerly well-off people suddenly rendered homeless by the Great Depression. They sarcastically toast the former president ("We'd Like to Thank You, Herbert Hoover"). The shanty town is broken up by the cops, who take Annie back to the orphanage.
At the orphanage, Miss Hannigan vents her frustration at being surrounded by children ("Little Girls"). Grace Farrell, the assistant to the billionaire Oliver Warbucks, comes to the orphanage, asking for an orphan to spend Christmas at his mansion. Seeing how poorly Miss Hannigan treats Annie, Grace insists on taking her.
At Warbucks's mansion, Grace introduces Annie to the staff and explains that she will have every luxury available ("I Think I'm Gonna Like It Here"). Oliver Warbucks returns, and isn't happy to have Annie in his mansion, having assumed all orphans were boys. Warbucks instructs Grace to take her to a movie while he works, but when he realizes that Annie has never seen New York, he decides to take her there himself, walking the 45 blocks to the Roxy and seeing New York City in all of its glory ("N.Y.C.").
Grace pays Miss Hannigan a visit to tell her that Warbucks wants to officially adopt Annie. Hannigan becomes furiously envious that the orphan she hated so much will suddenly have everything. Her ne'er-do-well brother Rooster and his girlfriend Lily drop by in hopes of a handout. When Miss Hannigan mentions that Annie is going to be adopted by Warbucks, Rooster realizes they can use this situation to their advantage ("Easy Street").
Having noticed a broken locket around Annie's neck, Warbucks buys her a new, more expensive one from Tiffany's. He wonders whether he is ready for such a big change in his life ("Why Should I Change A Thing?"). When he offers Annie the locket and attempts to take off the old one, Annie bursts into tears, as the locket was the only thing left to her by her parents, and she still holds out hope that they will return for her. Warbucks pledges to find her parents no matter what it takes, calling J. Edgar Hoover to get the Federal Bureau of Investigation on the job ("You Won't Be An Orphan For Long").
Annie appears on Bert Healy's radio show ("Maybe (Reprise)"), where Warbucks announces that he is offering $50,000 to the couple who can prove they are her parents. Healy then sings a song with the Boylan Sisters ("You're Never Fully Dressed Without a Smile"). At the orphanage, the girls are listening to the show. They joyously sing along ("You're Never Fully Dressed Without a Smile (Reprise)").
A couple claiming to be Annie's parents, Ralph and Shirley Mudge, arrive at the orphanage. In fact, they are Rooster and Lily in disguise. They believe they can pass themselves off as Annie's parents with Hannigan's help, for which she demands half of the money ("Easy Street (Reprise)").
Warbucks brings Annie to Washington, D.C., where she meets President Franklin D. Roosevelt. Roosevelt and his cabinet are inspired by her optimism and decide to make it a cornerstone of their administration ("Tomorrow (Cabinet Reprise)").
Once back home, Warbucks tells Annie how much he loves her ("Something Was Missing"). Because all the people claiming to be her parents were frauds, he offers once again to adopt her, and Annie gleefully accepts. The delighted staff get Annie dressed for the formal adoption proceedings, and tell of how her arrival has changed their lives ("Annie"). As Judge Louis Brandeis shows up to begin the adoption proceedings, Warbucks and Annie dance together ("I Don't Need Anything But You").
They are interrupted by Rooster and Lily in disguise. The two present faked documents, as well as the other half of Annie's locket, seemingly confirming their story. Warbucks requests that she be allowed to stay one more night, and they can take her away on Christmas morning. The next morning, Annie wonders if her life with her parents will really be as good as her life with Warbucks could have been ("Maybe (Second Reprise)"). Warbucks receives a surprise visit from Roosevelt and his Secret Service. The FBI has learned that Annie's parents are actually David and Margaret Bennett, who died some time ago; Annie truly is an orphan. Mr. and Mrs. "Mudge" show up to take Annie and the money, but are quickly exposed. They are arrested by the Secret Service, along with Miss Hannigan. Annie is adopted by Warbucks, who notes that this Christmas is the beginning of a new life for them, for the orphans (all of whom are adopted by wealthy friends of Warbucks), and for the rest of the country, thanks to Roosevelt's New Deal ("A New Deal for Christmas"/"Tomorrow (Second Reprise)").