The novel - "Go Set a Watchman" - was written in the mid-1950s and recently rediscovered. It is to be released in July, the publishing house said.
Lee won the Pulitzer Prize for "To Kill a Mockingbird" -- a searing tale of racism in the Great Depression-era South - in 1961.
The novel - standard reading in American classrooms for decades - has been translated into more than 40 languages.
The second novel is in many ways a sequel to "Mockingbird" and features many of the same characters around 20 years later, the publishing house said.
Lee, 88, said she was "humbled and amazed" that the manuscript was to be published after so many years.
"I hadn't realized it had survived, so was surprised and delighted when my dear friend and lawyer Tonja Carter discovered it," she said in a statement.
"After much thought and hesitation, I shared it with a handful of people I trust and was pleased to hear that they considered it worthy of publication."
"This is a remarkable literary event," said Jonathan Burnham, Harper publisher and senior vice president.
"The existence of 'Go Set a Watchman' was unknown until recently, and its discovery is an extraordinary gift to the many readers and fans of 'To Kill a Mockingbird'," he added.
"Reading in many ways like a sequel to Harper Lee's classic novel, it is a compelling and ultimately moving narrative about a father and a daughter's relationship, and the life of a small Alabama town living through the racial tensions of the 1950s."
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