An agency official says it landed about 40 kilometres southeast of the town of Senneterre.
The balloon was launched from Timmins, Ont., on Wednesday night and was in flight for 10 hours.
The driving distance between Timmins and Senneterre is approximately 400 kilometres.
A recovery team was sent to the landing site to retrieve hardware from the balloon, which was launched under a joint Canadian-French program.
Agency president Walter Natynczyk called it an historic launch that marks the beginning of a new opportunity for Canada.
In a prepared statement, he said the Canadian engineering and scientific communities will now gain valuable access to frequent flight opportunities starting in 2014.
It took two attempts to get the balloon airborne after a launch planned for Monday night had to be scrubbed due to unfavourable weather.
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.