The two said in statements posted on Instagram that they made the decision after “many meaningful and difficult conversations.”
A statement from the prime minister’s office said both have signed a legal separation agreement.
The couple were married in 2005. They have three children, 15-year-old Xavier, 14-year-old Ella-Grace and 9-year-old Hadrien.
“They remain a close family and Sophie and the prime minister are focused on raising their kids in a safe, loving and collaborative environment,” the statement from his office said. “The family will be together on vacation, beginning next week.”
His office requested respect for their privacy.
Trudeau is the second prime minister to announce a separation while in office.
His father, Pierre Trudeau, separated from wife Margaret in 1979, and the two divorced in 1984.
Justin Trudeau channeled the star power of his Liberal icon father when he first won office in 2015. Scandals, voter fatigue and economic inflation have taken a toll on his popularity after eight years in power.