The document did not provide details on the settlement, and a lawyer for the museum, Matthew Goforth, declined to comment Wednesday. He cited the terms of settlement negotiations.
An attorney for Lee did not immediately return a message seeking comment.
A judge would have to approve any settlement.
Lee, 87, has had a stroke and lives in Monroeville after years of splitting time between the town of 28,000 and New York.
Lee's lone published novel, released in 1960, tells the story of small-town lawyer Atticus Finch, his two children and the struggle against racial prejudice and injustice in the Jim Crow South. Considered a modern classic, the book was turned into a movie of the same name starring Gregory Peck.
The set for the movie's climactic courtroom scene recreated the Monroe County Courthouse, where the museum is located. The museum includes a gift shop that has sold book-related souvenirs including clothing.
The lawsuit said the museum took advantage of Lee's trademarks to sell souvenirs and wrongly used the title of the book as a website address without any compensation. The museum took in more than $500,000 in 2012, the lawsuit said. Goforth previously said the museum earned $28,566 from merchandise sales that year.
Lee filed the lawsuit after seeking a federal trademark for the title of her book when it is used on clothing. The museum opposed the application, saying souvenir sales were vital to its continued operation.
Now, the museum has changed its website name to http://www.monroecountymuseum.org . Items aren't offered for sale online. The site says the gift shop "offers dozens of custom items available ONLY in Monroeville."
The website says the shop has "a great selection of books and memorabilia about Harper Lee" and Truman Capote, a childhood friend of Lee who also lived in Monroeville and went on to write "In Cold Blood."