The indictment comes after a decades long investigation by the FBI.
Federal prosecutors say the shoes were stolen in 2005 from the Judy Garland Museum in Grand Rapids, Minnesota.
But they were recovered three years later during an FBI sting operation.
The suspect, Terry Martin, has been indicted on one count of theft of a major artwork.
The shoes are valued at about $3.5 million.
Judy Garland wore several pairs of the ruby slippers in "The Wizard of Oz."