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Gagne, 25, made his series debut at Laguna Seca this year, filling the vacancy created when compatriot Nicky Hayden was tragically killed in a cycling accident, and scored a pair of 15th-place finishes at the Californian track.
Bradl was forced to miss the second race at the most recent WSBK round at Portimao when he injured his right wrist in a highside crash in the first race in Portugal.
The German is set to undergo surgery on Thursday, ruling him out of this weekend's Magny-Cours races.
"Obviously I would like to thank Honda and the team for the opportunity to come back and get a second shot at World Superbike," said Gagne.
"Laguna Seca was a dream come true for me, and the knowledge and experience I gained from the team throughout that weekend was massive.
"It will also be nice to have some experience with this version of the Fireblade going into FP1.
"Magny-Cours is a completely new track for me but I look forward to the challenge of racing on a new circuit and continuing to learn and grow."
Gagne joins ex-Ducati rider Davide Giugliano for the Magny-Cours weekend, as the Italian makes his second outing of the year for Honda following last month's Lausitz round.
HRC test rider Takumi Takahashi stepped in for the most recent round at Portimao, and will also rejoin the Ten Kate squad in Jerez next month.
Portimao WSBK: Rea closes on title with another win
Bradl withdraws from remainder of WSBK season