It was originally designed to be a loop, starting near Toronto and running northeast to Peterborough, then southeast to meet the Grand Trunk Railway (GTR) on the banks of Lake Ontario.
By the time it had been built other lines had run into Toronto, so the GJR instead ran from Belleville to Peterborough, and then to Omemee where it met the Midland Railway of Canada.
The rapidly industrializing centre of Peterborough was a significant target for a series of proposed shortline railways, as it was mainly connected to the outside world through waterways.
A revival of these plans in the 1850s, however, saw the railway bypass Peterborough and cut ambitiously to the west, aiming for Lake Simcoe and Georgian Bay.
A bridge collapse in 1861 effectively terminated through traffic on the Cobourg and Peterborough line, restricting rail service to Peterborough to only operate via the Millbrook Branch – a branch line of a shortline – eliminating the direct connection to the Grand Trunk mainline at Cobourg.