It was the last of NASA's three surviving shuttles to retire when it completed its final flight on July 21, 2011.
Atlantis' predecessors, the Endeavour, Enterprise and Discovery, have all been transported to museums and a science centre in California, New York, and Virginia, respectively.
But Atlantis' final 16-kilometre journey lays to rest the last relic of the space-shuttle era, as NASA makes way for the next generation of spacecraft.
"This Shuttle Atlantis is the final shuttle to go on display for museums … It's a very significant milestone that the shuttles will go on display," said Lisa Malone, spokeswoman for NASA's Kennedy Space Centre. "And this is the final move."
Atlantis began its first mission on Oct. 3, 1985, where it spent four days in space delivering classified cargo, widely believed to be military communications satellites.
First shuttle to dock with Russian space station
Its key missions included carrying the Venus-bound Magellan probes and the Galileo probes into space in 1989. In 1995, Atlantis became the first shuttle to dock with the Russian space station Mir.
The shuttle will begin its journey from the Kennedy Space Center's Vehicle Assembly Building, where it has been since last month. There, technicians have been preparing Atlantis to go on display to the public. This included removing components and chemical systems inside the shuttle that may be toxic, said Malone.
The shuttle will be transported, slowly, atop a 76-wheel flatbed vehicle. It will pause along the route at roughly 10 a.m. for a retirement ceremony with officials including NASA administrator Charles Bolden, as well as current and former astronauts from Atlantis' final mission.
It is expected to reach the visitor complex at about 6 p.m. It will then be covered and protected while construction of the complex is completed, said Malone.
A grand opening of Atlantis' new home at the Kennedy Space Center Visitor Complex is planned for July 2013.
The $100-million US building will showcase Atlantis suspended in the air in the orbit position, with a massive digital projection of Earth that will rotate by the shuttle.