Sean grew up in the Chicago suburb of Glen Ellyn, Illinois. His father, Ron, a lithographer, left he and his four siblings when Sean was a young child. Sean says he hasn't seen his father in more than 10 years. His mother, Mary, works at a food bank. Sean attended Illinois State University where he he majored in performance and conducting. He supported himself through his college years by playing piano for voice lessons and working in community theater

Hayes began his professional career in the Chicago theatre community, serving as musical director at the Pheasant Run Theater for several years, appearing in several productions as well. He also appeared in the original production of "Role Play" at the Organic Theatre. An alumnus of the famed Second City improvisational comedy group, Hayes also had gigs as a stand-up comic, performing at The Comedy Club in Los Angeles.

While still in Chicago, Hayes won roles in television shows as well as the television movie A & P (1996), based on a story by John Updike, before landing the role which earned him an Emmy Award in 2001 - Jack McFarland on the hit NBC comedy series Will & Grace (1998). He has also been honored with a SAG Award, an American Comedy Award and a TV Guide Award as well as with two Golden Globe Nominations.

He played a stint with the Second City comedy troupe and then became a musical director for a local theater. He grew tired of that after a while and in the spring of 1995, moved to LA. He got a "hellish" job at a restaurant. His first big break was landing a national tour with Kenny Rogers for a Christmas show. In 1997 he got a series of commercials that gained him attention and led to his eventual role on "Will and Grace".

Hayes made his feature film debut in 1998 in the title role of the art-house hit Billy's Hollywood Screen Kiss (1998) which won critical acclaim at the Sundance Film Festival. He most recently starred in the box-office hit Cats & Dogs (2001) for the Warner Bros. Studios. Hayes made his home in Los Angeles.