Kanan received his big break working for Academy Award-winning Director John Avildsen in the 1989 film The Karate Kid Part III. The following year, he starred on the Fox television series The Outsiders. In 1993, Kanan joined the ABC soap opera General Hospital as A. J. Quartermaine and was nominated for an award in the Outstanding Newcomer category by Soap Opera Digest. He left the series abruptly in 1997 following his struggle with alcoholism.

In 1999, Kanan joined the cast of the NBC soap opera Sunset Beach as Jude Cavanaugh and remained with the show until its cancellation later that year. He wrote and executive-produced Chasing Holden, distributed by Lionsgate, which starred DJ Qualls. In November 2000, he joined the cast of the CBS soap opera The Bold and the Beautiful as Deacon Sharpe, playing a character that was originally conceived as a short-term villain. In 2002, rumors surfaced that the actor was fired, but he remained with the show until early 2005 when he opted to go on a recurring status, and he last appeared February 22, 2005.

While appearing on The Young and the Restless, he starred in the 2009 Indie film Abracadabra, which was directed by Julie Pacino (Al Pacino's daughter) and was screened at the Cannes Film Festival. In May 2010, Kanan appeared in My Trip to the Dark Side, written and directed by Shane Stanley. He later starred in the 2011 sequel My Trip Back to the Dark Side. That same year, Kanan wrote "The Modern Gentleman; Cooking and Entertaining with Sean Kanan", published by Dunham Books.

Sean and Michele Kanan married in July 2012. He has a daughter by his prior relationship and Michele has four children of her own. Politically Kanan is involved with the Anti-Defamation League. In May 2016 Kanan said that he supported Donald Trump for President of the United States.