In 1987, at 18, Shanahan was drafted second overall by the New Jersey Devils. His reputation was such that many people pegged him as a cornerstone player for the Devils franchise before he'd even played his first NHL game.

After his fourth season with New Jersey, the St. Louis Blues signed Shanahan as a free agent. Under league rules, St. Louis had to compensate the Devils, and an arbitrator ruled that the winger was worth no less than Blues captain and defensive star Scott Stevens. In his second year with St. Louis, Shanahan scored 51 goals. In addition to the offense he generated, Shanahan had proven that he was not afraid to mix it up if he felt the situation called for it. His statistics in 1993-94 epitomized his style as he scored 52 goals and logged 211 minutes in the penalty box.

In 1995 Shanahan got the shock of his career when he was traded to the Hartford Whalers. He was so popular in St. Louis that local TV stations interrupted regular programming to announce the news on the day of the trade. The Whalers, meanwhile, were ecstatic to be getting a player of Brendan's caliber.

Shanahan didn't take long to get over his disappointment with the trade, and he got ready to play the kind of hockey that would put fans in the seats. But even though he had a good 1995-96 season statistically, scoring 44 goals, the team continued to struggle on the ice and at the box office, and Shanahan asked to be traded. He wanted to play for a contending team whose fans were passionate about the game.

The Detroit Red Wings, who had been improving themselves through some smart trades and prescient drafting, were ready for just such a player to come along. Scotty Bowman had signed on as coach in 1994, and was looking for the final element he needed to make the Wings a Cup winner after they lost in the 1995 finals to New Jersey and the 1996 Western Conference finals to Colorado. Detroit paid a steep price trading forward Keith Primeau, defenseman Paul Coffey and a first-round draft pick to land Shanahan.

As if on cue, Detroit captured the Stanley Cup in 1997, the team's first championship in more than 40 years, by sweeping the Philadelphia Flyers, and they duplicated the feat in 1998 against the Washington Capitals. Over the next five seasons Shanahan continued his strong play with the Wings, reaching the 500-goal and 1,000 point plateau in 2001-02 while capturing his third Stanley Cup later that spring.

After nine years and three Stanley Cups with the Detroit Red Wings, Shanahan signed a one-year contract with the New York Rangers in the summer of 2006.

Upon his arrival in New York, Shanahan was named as an alternate captain of the club. In his frist game as a Ranger, he scored two goals including his 600th NHL career goal. Mid-way through that season however, in a game against the Philadelphia Flyers Shanahan was hospitalzied after a hard collision with the Flyers' Mike Knuble that left him unconscious on the ice for several minutes.

Shanahan returned to the Rangers line-up after missing only 15 games and continued to contribute offensively in his first year with his new club. New York would be eliminated in the second round of the playoffs that year, but Shanahan was welcomed back for the upcoming 2007-08 season. As a veteran forward in his second season in the Big Apple, Shanahan scored 23 goals in 73 games, his lowest total in a full year since his rookie season twenty years ago.

In the summer of 2008, the New York Rangers opted not to re-sign Shanahan and were rumoured as one of the teams looking to sign the unrestricted free agent Mats Sundin. The former Maple Leaf captain would eventually sign in Vancouver and Shanahan would shortly after sign as a free agent with the New Jersey Devils, the club that originally drafted the rugged forward in 1987.

On the international stage Shanahan represented his homeland on numerous occasions including the 1987 World Junior Championships, the 1991 Canada Cup, the 1994 World Championships, the 1996 World Cup, the 1998 and 2002 Winter Olympic Games.