The former South Korean international joined Vancouver in December 2011 and was named the team's player of the year in 2012.
Previously, he won two Dutch Eredivisie titles (2003, 2005) and a Dutch Cup title (2005) with PSV Eindhoven and was part of the Tottenham team that won the 2008 English League Cup.
He has also appeared in three FIFA World Cup appearances in his 13 year career, including a run to the semifinals of the 2002 tournament co-hosted by his home country.
Lee will be honoured prior to kickoff when the Whitecaps host Colorado on Sunday.
"It will be the most memorable game in my life," Lee said in a statement. "I'm a happy guy. I learned so many things throughout my career, much more than I had expected when I was young. It is a great time to finish with a great team and great people.
"I deeply appreciate our fans, my teammates, and all of the staff in the club. I'm sure Vancouver Whitecaps FC will remain in my mind as my team forever."
Lee will join the Whitecaps' front office after the season.