The museum will be located in the tourist-rich area surrounding Centennial Olympic Park and it's expected to draw up to 1.4 million visitors a year and to create 135 jobs in the state.
Mr. Perdue made the announcement at a biotechnology conference in San Diego and said it will enhance Georgia's reputation as a global hub for public health.
The state is already home to the federal Centers for Disease Control and Prevention as well as the American Cancer Society and other health-related nonprofit organizations.
There is no date yet for the museum's opening. It's designed to teach healthy living practices and will serve as a conference center for health-related events.
The National Health Museum's board picked Atlanta over several other cities including Washington. The Peach State got a boost from the board's chairman, Dr. Louis W. Sullivan, president emeritus of Atlanta-based Morehouse School of Medicine and a former secretary of the U.S. Department of Health and Human Services.
Mr. Perdue said the 190,000-square-foot museum will "give Georgians and visitors alike the opportunity to understand and experience the revolutions in health sciences that are helping people across the world live healthier lives."
Several sites around Centennial Olympic Park are under consideration. Once a warren of dilapidated warehouses, the area is now home to The Georgia Aquarium and the Coca-Cola Museum. CNN, which conducts tours for news junkies, is nearby.
A national civil rights museum is also expected to open in the area although plans are uncertain.
The health museum will be funded by a combination of personal, corporate, foundation and government contributors.
Gov. Sonny Perdue estimated the new museum will attract $230 million in initial investment to Georgia.