Wilkinson, 39, replaces Mark Parsons, who stepped down at the end of the National Women's Soccer League season to take over as head coach of the Netherlands national team.
Wilkinson played for the Thorns in 2015, her last professional season. She also played for the Boston Breakers in 2013, the league's first year.
She made 181 appearances with Canada and scored seven goals. She won bronze medals with the team at the 2012 and 2016 Olympics before retiring in 2017.
Wilkinson was an assistant for Canada in 2019 and 2020, and served under Great Britain head coach Hege Riise at the Tokyo Olympics last summer.
"Since leaving the field, Rhian has quickly accrued valuable coaching experience and knowledge at the international level, helping her stand out in a deep and competitive candidate pool," Thorns general manager Karina LeBlanc said in a statement. "She knows how to challenge players in an inspiring, motivating and honest way and she will bring integrity to the role, while being a player-first person and coach."