Wednesday night's launch was the second attempt after a launch planned for Monday night had to be scrubbed due to unfavourable weather.
The balloon was launched from Timmins, Ont., at 8:35 p.m. EDT and is to ascend to nearly 32 kilometres, and fly for about four to ten hours.
The agency says it should land in a 500 kilometre radius area from the launch site.
If the wind blows east, it could land in Quebec close to Rouyn-Noranda, Amos or Val d'Or. If it blows west, it could land close to the Ontario communities of Wawa, Kapuskasing, Chapleau or Sudbury.
The balloon is designed to give Canadian scientists a new platform to advance space science for up to 40 times less than the cost of a satellite or a launcher.
Stratospheric balloons can operate up to 45 kilometres in altitude, which is too low for satellites, too high for aircraft and cleared too quickly by rockets.
The Stratos Balloon Program is a joint effort of the CSA and the French space agency, the Centre national d'etudes spatiales.