Wakamatsu was a three-sport star at the Bay Area's Hayward High School in California, and ultimately chose baseball over football due to his lack of size. He and former Jacksonville Jaguars head coach Jack Del Rio (current head coach of the Oakland Raiders) were baseball and football teammates while there.
He was also an All-Pac-10 catcher during his last three years at Arizona State University, where he was a teammate of Barry Bonds and Alvin Davis. He was drafted by the New York Yankees as the last pick of the 1984 Major League Baseball draft, but decided to return to ASU.
Wakamatsu was drafted in the 11th round of the 1985 Major League Baseball draft by the Cincinnati Reds. He reached the Double-A level before the Reds released him before the 1989 season.
Shortly after the Reds released him, he signed with the Chicago White Sox, who assigned him to the Double-A Birmingham Barons. He spent 1990 and most of 1991 with the Triple-A Vancouver Canadians before getting his only call to the big leagues in May 1991. Wakamatsu played 18 games in the majors as a backup catcher for the White Sox in 1991, working in all of his starts for knuckleballer Charlie Hough.
After the 1991 season the White Sox granted Wakamatsu free agency, and he signed with the Los Angeles Dodgers shortly after. He spent 1992–1996 playing at the Double-A and Triple-A levels in the Dodgers, Texas Rangers, Cleveland Indians, Seattle Mariners and Milwaukee Brewers organizations before his playing career ended at age 33.
Following his playing retirement, Wakamatsu became a minor league manager in the Arizona Diamondbacks system, managing the Arizona League Diamondbacks in 1997, the Class-A High Desert Mavericks in 1998, and the Double-A El Paso Diablos in 1999. In 1998 he was named Manager of the Year in the California League, after leading the High Desert Mavericks to the playoffs.
He spent 2000 managing the Erie SeaWolves, the Anaheim Angels' Double-A affiliate, and then the next two seasons as a roving catching instructor in the Angels organization.
From 2003 to 2006, he was the Texas Rangers' bench coach. During the 2006 season, he served as manager for two games while Buck Showalter was in the hospital with an irregular heartbeat brought about due to dehydration, and in 2007, took the third base coach job when Ron Washington took over as manager. He spent 2008 as the bench coach of the Oakland Athletics.
On November 19, 2008, he was named the manager of the Seattle Mariners, replacing interim manager Jim Riggleman, and becoming the first Asian-American manager in the majors.
On April 6, 2009, Wakamatsu won his managerial debut as the Mariners beat the Minnesota Twins 6–1 on Opening Day.
Later in the season, Wakamatsu was officially selected as a coach under Tampa Bay Rays manager Joe Maddon for the 2009 MLB All-Star Game in St. Louis along with Kansas City Royals manager Trey Hillman on June 17, 2009.
Fred Claire, former baseball executive and current writer for MLB.com, stated that Wakamatsu and his staff, composed of bench coach Ty Van Burkleo, pitching coach Rick Adair, hitting coach Alan Cockrell, first base coach Lee Tinsley, bullpen coach John Wetteland and performance coach Steve Hecht, deserved credit for a 24-game improvement. Claire wrote this about Wakamatsu:
"It is the relationships that Wakamatsu has built during his time in baseball that defines him best. He was somewhat of an unknown to the public when he was hired as the Mariners' manager last November, but he is well-known and highly respected within the game."
On May 20, 2010, during a game against the Toronto Blue Jays, Wakamatsu received his first career ejection. As of June 12, he has a career total of two ejections.
On August 9, 2010, amidst one of the worst seasons in team history, Wakamatsu was fired as Mariners manager.
On November 8, 2010, Wakamatsu was announced as the new bench coach for the Toronto Blue Jays, under new manager John Farrell.
During 2013, Wakamatsu worked as a professional talent scout for the New York Yankees.
On October 25, 2013, Wakamatsu was announced as the new bench coach for the Kansas City Royals.
On April 19, Wakamatsu was one of five Royals (also pitching coach Dave Eiland, manager Ned Yost, pitcher Kelvin Herrera and shortstop Alcides Escobar) to be ejected in a game against the Oakland Athletics. Two games prior, Escobar had been injured following an attempt by A's third baseman Brett Lawrie to break up a double play. Considering the slide a dirty one, Royals pitcher Yordano Ventura hit Lawrie in the elbow the following game and was immediately ejected. In the series finale, A's pitcher Scott Kazmir hit Lorenzo Cain in the foot and warnings were given. Yost and Eiland were immediately ejected for arguing. Later in the 8th inning, Kelvin Herrera threw a 100 mph fastball behind Lawrie and a trio of ejections followed (Herrera, Wakamatsu and Escobar). The Royals would end up winning the game 4–2 despite the ejections. Wakamatsu was actually ejected twice, as when a warning has been issued, the pitcher and manager are automatically ejected. Wakamatsu was the acting manager. This was the cause of his first ejection, the second being him arguing with the home plate umpire.As of April 12, 2015
Wakamatsu resides in North Richland Hills, Texas with wife, Laura. Wakamatsu's sons, Jacob and Luke, are both also baseball players. Jacob was drafted by the Toronto Blue Jays in the 48th round of the 2011 MLB Draft and currently plays in the Kansas City Royals organization. Luke plays in the Cleveland Indians organization.
Born to a Japanese American father and an Irish American mother, he is fourth-generation Japanese American; and the first half-Asian and half-Caucasian manager in Major League Baseball history. Close friends and players call him "Wak" (pronounced wok). His father was born in the Tule Lake War Relocation Center, a Japanese American internment camp located in Northern California near the Oregon border.