Former coach Bev Priestman was suspended after New Zealand said Canadian staff flew drones over their training sessions before their opening match at the Paris Olympics.
In November, Canada Soccer said that Priestman would not return after an independent review found a "pattern of unacceptable culture" and lack of oversight.
Stoney most recently managed the NWSL side San Diego Wave and was named the league's Coach of the Year in 2022.
She will coach her first games for Canada at the Pinatar Cup in Spain next month.
"Together with the federation’s new leadership, we will strive to build on past successes and continue to grow the sport in Canada on and off the field," Stoney said in a statement. "I look forward to the journey ahead."
Canada won the Olympic gold in Tokyo and made it as far as the quarter-finals in Paris last year, despite being penalised six points due to the drone scandal.
"Casey’s track record of successful leadership, her values and strength of character, and her lifelong dedication to the advancement of women’s football make her the right person to lead our national team into its next chapter," Canada Soccer CEO and General Secretary Kevin Blue said.
