Pierce acted in such films as Crossing Delancey (1988), The Fisher King (1991), Sleepless in Seattle (1993), Wolf (1994), Nixon (1995), Down with Love (2003), and The Perfect Host (2010).

He portrayed Henry Newman in the comedy film Wet Hot American Summer and reprised his role in two series from Netflix in 2014 and in 2017.

He has since acted in the CBS legal drama The Good Wife (2014–2015), the ABC docu-drama When We Rise (2017), and the HBO Max series Julia (2022–23).

After his graduation, Pierce moved to New York City, where during the 1980s and early 1990s he was employed in various jobs, such as selling ties at Bloomingdale's and working as a security guard, while pursuing an acting career and studying at Michael Howard Studios.

During this period he played Laertes in an off-Broadway production of Hamlet, with Kevin Kline in the title role, and made his Broadway debut in 1982 in Christopher Durang's Beyond Therapy.

[14] For his work on Frasier, Pierce was nominated for a Best Supporting Actor Emmy a record eleven consecutive years, winning in 1995, 1998, 1999 and 2004.

David Bianculli of New York Daily News declared, "Not since Jack Benny has TV seen such a great reactive comedian as Pierce, and whenever he and [Kelsey] Grammer share the same stage, Frasier is undiluted magic.

[15] Pierce also appeared alongside Jodie Foster in Little Man Tate, with Anthony Hopkins in Oliver Stone's Nixon (1995), and with Ewan McGregor in Down With Love (2003).

[12] He provided the voice for Doctor Doppler in Disney's 42nd animated feature, Treasure Planet; Slim, a stick insect in Pixar's A Bug's Life; and Abe Sapien in Guillermo del Toro's Hellboy.

In his role in Sleepless in Seattle (1993), Pierce played the brother of Meg Ryan's character, a professor at Johns Hopkins University.

[12] Pierce declined to be credited for his Hellboy role because he felt it was the performance of Doug Jones, and not his own voice, which ultimately brought the character of Abe Sapien to life.

His commercial voiceover work included ads for the Tassimo coffee system, Seattle's Metro Transit, and home furnishings retailer IKEA Canada.

[12] In August and September 2006, he starred as Lieutenant Frank Cioffi in Curtains, a new Kander and Ebb musical staged at the Ahmanson Theatre in Los Angeles.

"[19] On November 19, 2007, Pierce was awarded an honorary Doctor of Fine Arts degree from Niagara University in Lewiston, New York.

[24] In 2020, Pierce replaced Tom Hollander as Paul Cushing Child in the biographical series Julia which premiered on HBO Max in March 2022.

Pierce acted alongside Bobby Cannavale, Amber Gray, Rachel Bay Jones, Denis O'Hare, and Steven Pasquale.

"[28] After years of media speculation about his sexuality, Pierce revealed in 2007 that he is gay and later confirmed through his publicist that he and television writer, director and producer Brian Hargrove were a couple.

He has appeared in Washington, D.C., to testify in support of expanding funding for treatment, and he publicly campaigned for the National Alzheimer's Project Act.

Pierce told MSNBC in 2011, "it is up to us, to all of us, to the American people and to their representatives about whether we face the challenges and make all the effort necessary or if we ignore it and just let this sort of tidal wave crash over us.