Archaeologists from Upplandsmuseet, the musem of Uppland north of Stockholm, found the stone at Hagby church.
Dating from the mid-1000's, it was used as the threshold to the armory at Hagby church in the Middle Ages.
Its existence was documented as recently as the 17th century.
But when the church was demolished in the 1830s, the stone vanished and its fate remained unknown until now, the museum said in a press release.
"It's very rare that we find unknown or missing rune stones today," said Emelie Sunding, the museum archaeologist who found the stone.
In Sweden there are about 2,700 known Viking rune stones, with more than 1,300 in Uppland, but many of these are smaller fragments.
"It's very rare that we find whole rune stones," said Sunding.
The discovery is also important as the work of Foot was previously known only through reproductions.
The carving includes many parallels with jewellery of the same period.