Ellison, a Democrat, contacted the Library of Congress about the Koran last month, said Mark Dimunation, chief of the rare book and special collections division at the library.
Dimunation will walk the Koran across the street to the Capitol building for the swearing-in, and then walk it back to the library.
The Koran, an English translation of the Arabic, was published in 1764 in London, a later printing of one originally published in 1734.
"This is considered the text that shaped Europe's understanding of the Koran," Dimunation said.
It was acquired in 1815 as part of a 6,400-volume collection that Jefferson, the third U.S. president, sold to replace the congressional library that had been burned by British troops the year before, in the War of 1812.
Ellison was en route to Washington and unavailable for comment Wednesday, but his spokesman, Rick Jauert, said that the Ellison "wants this to be a special day, and using Thomas Jefferson's Koran makes it even more special."
"Jefferson's Koran dates religious tolerance to the founders of our country," he added.
Some critics have argued that only a Bible should be used for the ceremonial swearing-in. And last month, Rep. Virgil Goode, a Republican, warned that unless immigration is tightened, "many more Muslims" will be elected and follow Ellison's lead. Ellison was born in Detroit and converted to Islam in college.
Jefferson collected books in all topics and languages, said Dimunation. The Koran survived an 1851 fire in the Capitol building. Dimunation described it as a two-volume work, bound in leather with marble boards.
"As a rare book librarian," he said, "there is something special about the idea that Thomas Jefferson's books are being walked across the street to the Capitol building, to bring in yet another session of governmental structure that he helped create."