Two sets of remains were discovered just under the surface of the road on South Church Side next to Hull Minster.
Prayers were said at the roadside before the bones were reinterred in the church's crypt on Tuesday afternoon - where they should now rest for perpetuity.
Interim Minister Bishop Frank White said a small part of the churchyard was sold to the predecessor to Hull Council in the 1850s to allow them to widen what was then a lane.
Bishop White said: "What they discovered when they started planing the road was both the old churchyard wall which was right in the middle of the present South Church Side and these two burials, which clearly hadn't been removed when the Corporation in the 1850s had bought that corner of the churchyard and cleared the burials."
The section of the road where they were found was shuttered off while legal permission was sought to remove the remains.
The church dates back to about 1300 and its churchyard was the main burial site for the city for centuries.
The remains are thought to date from around the 1850s.
A spokeswoman for Hull Council said: “Whilst carrying out essential road improvement works to South Church Side, remains from two historic burials were found at a shallow depth.
“We have been working closely with the Humber Archaeology team who have carried out an investigation of the burials.
"The remains have been recorded and transferred to the Hull Minster crypt.
“The road scheme has now been redesigned and Humber Archaeology will supervise the ongoing works.”