Minnesota announced Whalen's return to coach her alma mater on Thursday. Her deal is pending approval by the school's board of regents.
"I have so many special memories at the University of Minnesota. I can't tell you how excited I am to have the opportunity to make more," Whalen said in a statement. "Becoming the head coach here at the U and being a Gopher again is a dream come true. At every level, basketball has given me so much. I've learned from so many great players, coaches and mentors, and now I have a chance to share that knowledge and help shape the new generation of Gopher stars. I'm ready to get started."
Whalen will replace Marlene Stollings, who left to become head coach at Texas Tech.
Whalen, who has been a member of the U.S. women's team since 2002, announced in February that she was retiring from international competition.
As a player at Minnesota, she became the first three-time All-American in program history and was the school's all-time points leader when she finished her college career.
"People talk about the 'it' factor, and that is always difficult to define, but everyone who has ever spent time around Lindsay Whalen knows she has it," Minnesota athletic director Mark Coyle said in the statement. "She has excelled at everything she has ever done in her life because she's unflappable, determined and has a legendary work ethic. She's played for some of the top coaches in the world, she's competed at the highest levels the sport has to offer, and I know she will be a great head coach for our women's basketball program."
Whalen, 35, has played for the Lynx for the past eight seasons. She averaged 8 points, 4.1 assists and 2.5 rebounds in 22 games last season. She is a five-time All-Star and has a 11.9 points per game average in 448 games over 14 seasons with the Connecticut Sun and the Lynx.