The discovery was made by the Exeter Office of Cotswold Archaeology who are working with Kier ahead of construction of a new bus station and leisure complex.
The council said archaeology work will not impact on the construction timetable for the £52m scheme.
The finds include coins and local pottery made in the area for the military, as well as fine red Samian tableware imported from France.
Experts said ditches uncovered during digging belong to a new, and completely unknown, Roman military site.
Andrew Pye of Exeter City Council said: “This is a very important, and completely unexpected, discovery, in an area that has been heavily changed by previous post war redevelopment.
“Along with other recent work in Exeter, it demonstrates just how much of the city’s history can still survive in unlikely places, despite damage caused by bombing and modern concrete foundations.
“As the city continues to grow and renew, it is a good example of how the planning system and developers work together to make sure that remains that are inevitably affected by new development are properly excavated and recorded for the benefit of this and future generations.”
Derek Evans, of Cotswold Archaeology’s Exeter Office, said: “We’re very pleased to be working with Kier and Exeter City Council on this important site.
“The unexpected nature of this discovery and the significance of uncovering previously-undocumented Roman military features in this area of the city, have made this a challenging and interesting project.
“We look forward to undertaking further analysis of the finds and other material recovered during our works and refining the story of the site’s history.”