Archaeologists from Norfolk County Council made the surprise discovery as they excavated land, off the Croxton Road, which is due to be developed.
The adult and juvenile skeletons date from about the 13th century and prove for the first time there was a medieval burial site in that part of the town.
Archaeologists are excited the discovery could provide evidence of a church or chapel that has not appeared in any historical records.
Jayne Bown, from the Norfolk Archaeological Unit, said: "This excavation has added to our knowledge about the medieval period in Thetford.
"Although we did expect to find some human remains during the excavation, we were excited to find evidence of a burial ground.
"The location of the burial ground raises even more questions – was there a nearby chapel or church, which we do not know about?"
The skeletons were excavated by six archaeologists and have been removed for further tests, to see what gender they are and how they died.
Other discoveries made during the excavation include storage pits, walls and posts.
Ms Bown said: "For a small area, we found quite a lot of finds, which will help us understand about medieval life in the town."
The archaeologists have completed their excavations and Abel Development is now working on the site.