Born on February 16, 1987, Bourdon was an only child raised by his mother, Suzanne Boucher, in the small French-speaking community of Shippagan, New Brunswick. When he was nine, he was confined to a wheelchair after being diagnosed with juvenile arthritis, which he later overcame. As a teenager, he attended École Marie-Esther Secondary, where he was a straight-A student. Growing up in a fishing town, he worked summers on his uncle's crab fishing boat.

He played as a 13- and 14-year-old with the Peninsule Acadien Lynx, and with the Miramichi Rivermen from ages 15–16, both local minor ice hockey teams. After being the third overall choice in the 2003 QMJHL draft, Bourdon left home when he was 16, returning in the off-season to live with his mother. Upon turning professional and signing his first contract, he anonymously donated C$10,000 to the local minor hockey association for families who could not afford equipment. His donation was posthumously revealed by his former bantam hockey coach, Gilles Cormier, who managed the local arena at the time of Bourdon's death.

Bourdon joined the Val-d'Or Foreurs for the 2003–04 season, registering eight points in 64 regular season games and scoring one goal in seven playoff games. He appeared in all 70 games with the Foreurs in 2004–05, scoring 13 goals and 19 assists, and participated in the CHL Top Prospects Game, an exhibition for draft-eligible players. In June 2005, Bourdon was the tenth pick overall, selected by the Vancouver Canucks, at the 2005 NHL Entry Draft. Ranked sixth overall for North American skaters coming into the draft, Bourdon was noted as a physical two-way defenceman with significant offensive skills and a strong shot, as well as an excellent skater. He was the second Shippagan-born hockey player to be drafted in the NHL, after goaltender Yanick Degrace was drafted by the Philadelphia Flyers in 1991.

Invited to the Canucks training camp, Bourdon almost made the team as an 18-year-old, but instead was returned to the QMJHL for further development. He began the 2005–06 season with the Foreurs, registering 20 points in 20 games, before being traded to the Moncton Wildcats, who were hosting the 2006 Memorial Cup. In exchange for Bourdon, the Wildcats sent Ian Mathieu-Girard, Jean-Sébastien Adam, a fourth-round pick, and a first-round selection in 2008 to Val-d'Or. Shortly after the trade, Bourdon injured his ankle, suffering a fractured fibula, high and low sprains, and a second-degree ligament tear. Although he returned to join Moncton in the playoffs, doctors told him that it would take two years to fully recover. He managed a full recovery after one year, but his turning ability and backwards skating sometimes lagged. Competing in the Memorial Cup, he reached the Canadian Hockey League (CHL) final with the Wildcats, who lost 6–2 to the Quebec Remparts.

After signing a three-year contract, worth $850,000 per year with the Canucks on May 4, 2006, Bourdon earned a spot on the team's 2006–07 opening roster. He played his first NHL game on October 10, 2006 against the Minnesota Wild, but after playing nine games and scoring no points, he was sent again to the QMJHL for further development. On January 8, 2007, Bourdon was again traded in the QMJHL, with Moncton sending him to the Cape Breton Screaming Eagles in exchange for Mark Barberio and a first round selection in the 2007 QMJHL draft. As a Screaming Eagle, Bourdon lost in the QMJHL semi-final against his former team, Val-d'Or. He finished the 2006–07 QMJHL season with 20 points in 36 games. When the Canucks did not qualify for the playoffs, they sent Bourdon to play five games for the Manitoba Moose, who were in the middle of the AHL playoffs. He was held pointless through five AHL playoff games. Including his participation in the 2007 World Junior Championships, Bourdon played for five different teams throughout the 2006–07 season.

Initially failing to make the Canucks starting roster out of training camp, Bourdon began the 2007–08 season with the Manitoba Moose; however, because of a series of injuries among the Canucks' defencemen throughout the season, Bourdon was called up on several occasions. Bourdon scored his first goal on November 16, 2007, against goaltender Niklas Bäckström in a 6–2 win over the Minnesota Wild. Bourdon finished the season on the Canucks roster, and was sent back to the Manitoba Moose for the AHL playoffs, playing in six playoff games for the Moose. He appeared in 27 games for the Canucks over the season, scoring two goals, as well as scoring 14 points during 41 games with the Moose.

As a young and promising defenceman, Bourdon was regularly mentioned in rumours of trades for more offence at the forward positions. Most significantly, he was speculated to be part of a package in exchange for Tampa Bay Lightning forward Brad Richards. Although Bourdon had a powerful shot, he did not play defence responsibly enough to earn a regular spot on the roster. He began to show signs of improvement and maturity as the Canucks used him more in the 2007–08 season.

Bourdon made his international debut representing Team Canada in the 2005 World Under-18 Championships, held in the Czech Republic, earning one assist in a silver-medal effort.