A two-time MLS Defender of the Year, Bocanegra also played professionally in England, Scotland, France, and Spain.

Prior to attending UCLA, Bocanegra was offered scholarships for American football but opted for soccer, which he thought of choosing as his career.

Bocanegra was signed by Fulham in January 2004, quickly becoming a fan favorite, garnering the nicknames the Jackal and the Black Snake.

[9] On September 1, 2007, Bocanegra captained Fulham for the first time in a Premier League match, a come from behind 3–3 draw with Tottenham Hotspur.

[21] On August 17, 2011, Bocanegra joined Scottish Premier League side Rangers, signing a three-year deal for an undisclosed fee.

[22][23] Bocanegra made his debut for Rangers against NK Maribor on August 18, 2011, in a UEFA Europa League qualifier.

His involvement in this match later caused controversy when Maribor filed a complaint to UEFA regarding the eligibility of Bocanegra's appearance, questioning whether he had the required clearance and paperwork.

[28] Bocanegra quickly became a fan favorite after a series of solid and impressive performances alongside his center-back partner, Dorin Goian.

[32] During an Old Firm 3–2 victory, on March 25, 2012, Bocanegra received a straight red card after fouling Georgios Samaras, conceding a penalty.

[33] After Rangers FC went into administration, in June 2012 the company's assets, including the players' contracts, were purchased by Charles Green's consortium.

Although many players departed because of this, Bocanegra's future was uncertain after not attending training,[34] as he wanted to leave in order to play at a higher level.

[35] A few weeks later, on July 29, 2012, McCoist appointed Bocanegra captain for the first round of the Challenge Cup- a 2–1 win over Brechin City.

After being dropped by the national team,[38] Bocanegra joined Racing de Santander on a season-long loan in an attempt to keep his international career alive.

[41] However, his time at Santander was considered "disastrous",[citation needed] as he failed to start the remainder of the matches, though still played regularly, coming on as a substitute.

Chivas USA traded up the allocation order with Toronto FC to land his signature, sending a first-round 2015 MLS SuperDraft pick and an international slot to the Canadian club.

[46][47] Bocanegra played for the United States at the 1999 FIFA World Youth Championship and earned his first senior cap for the U.S. on December 9, 2001, against South Korea.

Bocanegra's further exclusion from qualification, in part due to his unstable club situation, led to the appointment of Clint Dempsey as captain of the USMNT.