The sculpture was originally commissioned and placed at the ground by former owner Mohamed Al Fayed in tribute of his friend and global popstar Jackson following his death in 2009.
In September, it was removed by new owner Shahid Khan and taken to a warehouse owned by Al Fayed before getting picked up by the museum.
According to the Daily Mail, the sculpture will be housed near to the entrance of the Manchester-based museum in the Urbis Building.
"The National Football Museum is a splendid institution," said Al Fayed. "The statue means a great deal to me and my family. But on reflection, I decided it should go to a place where it can be enjoyed by the greatest amount of people for ever.
"I think Michael would have approved of the choice. Like football itself, he entertained the world."
Former Fulham boss Martin Jol was reported to have held talks with Al Fayed over buying the statue for £20,000, but talks are said to have broken down after he was sacked last December.