The move is pending receipt of Kobayashi's international transfer certificate and visa.
The 29-year old native of Fuji, Japan, spent the past two seasons with Shimizu S-Pulse of the J. League Division 1, appearing in 38 matches.
"I'm very happy to come to Vancouver and play for the great fans of this city," Kobayashi said in a statement. "I look forward to giving my all to help this club continue to grow and succeed."
Prior to his stint with Shimizu, the five-foot-10, 150-pound midfielder spent 18 months with Greek Football League side Iraklis FC, appearing in 14 matches.
In 2009, Kobayashi played with Stabaek Fotball of the Tippeligaen, the top tier of Norwegian soccer.
From 2006 to 2008, the Japanese international played three seasons with J. League Division I side Omiya Ardija. In 90 matches with Omiya, Kobayashi scored 14 goals.
Prior to joining Omiya, Kobayashi appeared in 104 matches for Tokyo Verdy, helping his team win the Emperor's Cup in 2004 and Japanese Super Cup in 2005.
Kobayashi has made one international appearance for Japan in a friendly against Trinidad and Tobago in 2006.