In 1999, while still at NYU, Morrison appeared on Late Show with David Letterman and Total Request Live as one of five members of the fictional parody boy band “Fresh Step”, an act that was conceived by several Late Show writers. The choreographer hired for “Fresh Step” was also the choreographer for the Broadway musical Footloose, and helped Morrison to get cast in Footloose later that year. Morrison dropped out of NYU to begin appearing in the show.

In 2001, Morrison was recruited to complete the quartet for the band LMNT. Morrison was replaced instead by Jonas Persch by the time its first album was released. Morrison commented in an interview about his experience in the boy band by remarking, “It was the worst year of my life. You know when you’re a performer and you’re out there on stage and you’re embarrassed that you’re doing something wrong. It was pretty bad.”

Morrison briefly appeared in a revival of The Rocky Horror Show in 2002. He then starred in the original cast of the musical Hairspray as Link Larkin from its opening in 2002 through January 2004. In 2005 Morrison changed gears, playing the role of Fabrizio Nacarelli in Adam Guettel’s The Light in the Piazza. Morrison was nominated for a Tony Award for his performance. He left the show on August 28, 2005.

Morrison started working in television, guest-starring on shows such as Ghost Whisperer, Numbers, CSI: Miami and Hack. Morrison also had small roles in films including Marci X (2003). He also appeared as Sir Harry in the 2005 ABC-TV production of Once Upon a Mattress, starring Tracey Ullman, Zooey Deschanel and Carol Burnett.

Morrison joined the cast of the CBS soap opera As the World Turns as Adam Munson on October 24, 2006, but left abruptly soon after due to a “scheduling conflict,” last airing on the soap on November 27. Morrison appeared in a benefit performance celebrating Andrew Lippa, and the 25th Anniversary of the performing troupe ‘The Kids in the Hall’ at the Orange County Performing Arts Center in Costa Mesa, California in December 2006. The performance benefited The California Conservatory of the Arts, a non-profit arts education organization focusing on pre-professional training for young students, grades six through twelve, in Orange County, California.

Morrison became engaged to actress Chrishell Stause on December 9, 2006. Their relationship later ended.

He earned a Drama Desk Nomination for his role in the Off Broadway show 10 Million Miles which ran at the Atlantic Theater Company in 2007. That same year he appeared in two films: Dan in Real Life, followed by Music and Lyrics as Cora Corman’s manager. In 2008, he played Lieutenant Cable in a Lincoln Center production of the musical South Pacific. He left the production at the end of 2008 and in early 2009 returned to California to shoot the first season of Glee.

Morrison played Will Schuester in the Fox Broadcasting television series Glee, which had its television preview on May 19, 2009. Schuester is a high school Spanish (later History) teacher who takes on the task of restoring the school’s glee club to its former glory. He made his directorial debut with the third season’s ninth episode.

In January 2010, Morrison signed a solo record deal with Mercury Records. His first studio album, Matthew Morrison, was released on May 10, 2011. Two singles were released from the album, “Summer Rain” and “Still Got Tonight”. The album also includes duets with Elton John (a medley of “Mona Lisas and Mad Hatters” and “Rocket Man”), Gwyneth Paltrow (“Over the Rainbow”) and Sting (“Let Your Soul Be Your Pilot”). On June 16, 2010, Morrison joined Leona Lewis—appearing at London’s O2 Arena as part of her world tour—for a one-off performance to sing “Over the Rainbow”.

In 2011, Morrison began dating Renee Puente. On June 27, 2013, Elton John helped Morrison announce that Morrison and Puente were engaged. Morrison and Puente were married on October 18, 2014, at a private home on the island of Maui. On May 16, 2017, it was revealed on his personal Instagram account that he and Puente were expecting their first child. Their son was born in 2017.

In March 2012, Morrison was featured in a performance of Dustin Lance Black’s play, 8—a staged reenactment of the federal trial that overturned California’s Prop 8 ban on same-sex marriage—as Paul Katami. The production was held at the Wilshire Ebell Theatre and broadcast on YouTube to raise money for the American Foundation for Equal Rights.

A Morrison concert at Connecticut’s Bushnell Center was recorded and aired on PBS in June 2013. On April 28, 2013, Morrison made his first major appearance in the United Kingdom as a guest performer at the 2013 Laurence Olivier Awards at the Royal Opera House in London. On June 4, 2013, 222 Records released Morrison’s second studio album, Where It All Began, an album of show tunes and jazz standards. One single was released from the album, a cover of “It Don’t Mean a Thing”.

Morrison returned to Broadway as J. M. Barrie in the Broadway debut of the musical Finding Neverland, which opened in April 2015.

On July 7, 2016, Morrison appeared alongside Megan Hilty in a summer evening of Broadway and other songs with The New York Pops at the Forest Hills Stadium in Forest Hills, Queens.

Since 2019, Morrison has been a “dance captain” on BBC One’s The Greatest Dancer alongside Cheryl, Oti Mabuse and in the second season, Todrick Hall as well. In the second half of 2019, he portrayed Trevor in the ninth season of the FX horror anthology television series American Horror Story.