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As a youth, Whitney played in the 1997 Quebec International Pee-Wee Hockey Tournament with a minor ice hockey team from South Shore.
Whitney enrolled at Thayer Academy, a college-prep school in Braintree, Massachusetts, in 1998, and logged significant playing time with their hockey team. Head Coach Jack Foley often paired Whitney, a freshman, with senior Brooks Orpik, his future rival in college (being on separate ends of the Boston College-Boston University Rivalry), and later his teammate on the Pittsburgh Penguins. Whitney's size and skill drew the attention of the USA Hockey National Team Development Program. After initially resisting the programs invitations, he left Thayer for the program, based in Ann Arbor, Michigan, for his senior year of high school.
A year later, he would play in the 2001 IIHF U18 Championships. Whitney picked up a single assist, in six games, as the United States finished in sixth place.
After graduating from high school, Whitney accepted a full scholarship to play for Boston University under Jack Parker. In his freshman year, he recorded 21 points in 35 games and was named to the 2002 Hockey East All-Rookie Team. He was then selected by the Pittsburgh Penguins, as the fifth overall pick in the 2002 NHL Entry Draft. Upon completing his third year with Boston, he opted to forgo his senior year of college eligibility to turn professional. He was subsequently assigned by Pittsburgh to their American Hockey League (AHL) affiliate, the Wilkes-Barre/Scranton Penguins, for the 2004 Calder Cup Playoffs. He played in 20 games, recording 10 points, however, Wilkes-Barre/Scranton was defeated by the Milwaukee Admirals in the finals.
He would also play the following year in the 2003 World Juniors. Whitney posted better numbers than the year previous, picking up five points (one goal and four assists) in seven games, as the United States finished in fourth place.
Whitney made his NHL debut with Pittsburgh in the 2005–06 NHL season, playing in 68 games. He was called up on October 31, 2005, to replace injured defenseman Dick Tärnström and remained on the team until the season ended. His first NHL goal came on December 1, 2005, against Henrik Lundqvist of the New York Rangers. Whitney finished the season with six goals and 32 assists.
During the 2007 off-season, Whitney signed a six-year, $24 million contract with a no-trade clause, avoiding his pending restricted free agency. His offensive production dropped in the subsequent 2007–08 season, posting 40 points in 76 games. However, the Penguins finished second in the Eastern Conference and Whitney contributed six points in the 2008 Stanley Cup Playoffs, as Pittsburgh made it to the Finals against the Detroit Red Wings. Pittsburgh was defeated in game six of the series on June 4, 2008.
In the 2008 off-season, it was revealed that Whitney had been suffering from a chronic foot injury throughout the season. It was later discovered Whitney was born with abnormally high arches (hollow foot) in both of his feet. After an attempt using orthopedic inserts in his skates failed, Whitney underwent osteotomy, a surgical procedure to realign the bones in his left foot, on August 15, 2008. It was expected Whitney would miss five months of the 2008–09 season. After playing one game with Wilkes-Barre/Scranton, as part of a conditioning stint, Whitney made his return to Pittsburgh, in a 2–0 loss to the Tampa Bay Lightning, on December 23, 2008.
On February 26, 2009, Whitney was traded to the Anaheim Ducks in exchange for Chris Kunitz and Eric Tangradi. He scored one goal and five assists during the 2009 Stanley Cup playoffs, as the Ducks made it to game seven of the Western Conference Semi-Finals, losing to the Detroit Red Wings.
On March 3, 2010, Whitney was traded along with a 2010 sixth round draft pick (Brandon Davidson) to the Edmonton Oilers in exchange for defenseman Ľubomír Višňovský. The deal marked the second time that Whitney had been traded within a year, even though he has a no-trade clause in his contract.
Whitney underwent a second osteotomy in May 2010, this time to realign the bones in his right foot.
On December 28, 2010, in a game against the Buffalo Sabres, Whitney suffered from a right ankle injury. It was later announced that Whitney would miss the remainder of the 2010–11 season, needing surgery.
With injuries to fellow defensemen Paul Martin and Mike Komisarek, Whitney was selected as a replacement to represent the United States in the 2010 Winter Olympic Games, held in Vancouver, British Columbia. This marked Whitney's first time as an Olympic competitor. He and his team were runners-up and won the Silver Medal. It was Whitney's former teammate, Sidney Crosby, who scored the game-winning goal, which saw Canada defeat the United States 3–2, in overtime. Whitney played in all six games, not collecting any points.
On April 28, 2013, it was announced Whitney would not be returning to the Oilers for a fifth season.
On September 29, 2013, Whitney signed a one-year contract with the Florida Panthers. Whitney appeared scoreless in seven games with the Panthers to begin the 2013–14 season before on November 8, 2013, he was placed on waivers. Unclaimed, Whitney was assigned to the Panthers' AHL affiliate, the San Antonio Rampage, for the remainder of the season.
Whitney was an unrestricted free agent following the 2013–14 season. After failing to sign a contract with an NHL team, Whitney made a move to the Kontinental Hockey League (KHL) and on October 16, 2014, he signed a contract with HC Sochi. In the 2014–15 season, Whitney scored 19 points in 42 games in the inaugural season for Sochi. As a free agent, Whitney left Russia after one season and signed a one-year contract with Swedish club Modo Hockey of the SHL on June 24, 2015. Whitney announced his retirement on September 20, 2015 via Twitter.