Jue is known for his performances on Broadway, in national tours, off-Broadway and in regional theatre, particularly in the San Francisco Bay Area and at The Muny in St. Louis.

[1] Jue's off-Broadway credits include Dr. Mendel in the 2006 National Asian American Theater Festival's revival of William Finn's Falsettoland; numerous roles with the New York Shakespeare Festival in Hamlet, King Lear, The Tragedy of Richard II, Pericles, Prince of Tyre, Timon of Athens and The Winter's Tale; Dream True: My Life with Vernon Dixon (Vineyard Theatre);[2] Oscar in Chay Yew's A Language of Their Own (2005);[8] the father in Kevin So's musical, Victor Woo: The Average Asian American;[2] and Vice-Principal Huang in No Foreigners Beyond This Point, by Warren Leight (2005).

"[13] In 2009, after recovering from a back injury sustained in a 15-foot fall during rehearsals for a production of A Midsummer Night's Dream,[14] Jue appeared in Coraline with MCC Theater at the Lucille Lortel Theatre in the role of Father.

[17] In early 2014, Jue played the title character's father off-Broadway in Signature Theatre Company's premiere of Hwang's Kung Fu.

[20] From October to December 2018, Jue appeared in Wild Goose Dreams, a new play by Hansol Jung, at the Public Theater,[21] receiving another Obie Award for his performance.

[30] Jue created the role of Howard in Audible Theater's Good Enemy, by Yilong Liu, at the Minetta Lane Theatre in October and November 2022.

");[34] the narrator in Into the Woods, which he also choreographed, at TheatreWorks (2006, Bay Area Critics Circle Award; "Jue ... shows his amazing physical acting talent.

[40] That fall, he starred as Dr. Givings in The Actors Theatre production of In the Next Room (or The Vibrator Play) in Phoenix, Arizona (for which he won a ZONI award).

CBS St. Louis wrote: "The consummate acting, dancing and singing skills of Francis Jue as Sebastian are a joy to experience.

"[43][44] In early 2012, he appeared in The Winter's Tale at Yale Repertory Theatre[45][46] and returned to The Muny that summer in Thoroughly Modern Millie (this time as Ching Ho)[47] and Kassim in Aladdin.

[49] Jue appeared as Salvatore "Sally" Camatoy in a stage adaptation of Paper Dolls, by Philip Himberg, at the Tricycle Theatre in London from 28 February 2013 to 13 April 2013.

[50] The Times commented, "At [the musical's] heart is the relationship (which repeatedly made me cry) between Chaim ... and the wonderful Francis Jue as Salvatore – 'Sally'.

A review in The Boston Globe commented: "Jue delivers an indelible portrait of a Mephistophelean hustler who doesn’t so much walk as slither, a cannily corrupt survivor adept at switching allegiances.

[57] In early 2016, Jue played sushi master chef Koji in Tokyo Fish Story by Kimber Lee at Theatreworks.

[14] A reviewer for The San Diego Union-Tribune commented that in Wild Goose Dreams at La Jolla Playhouse in September and October 2017, "Jue portrays the father with a winning, playfully comic touch".

[63] In 2022, with Yale Repertory Theatre, he starred in Today is My Birthday by Susan Soon,[64] and with San Francisco Opera, he played Monk in Dream of the Red Chamber.

[75] In 2021, Jue starred in San Francisco Mime Troupe's radio serial "Tales of the Resistance, Volume 2: Persistence", Episode 2.