Rubin-Vega performed in the Broadway musical Rent with Wilson Jermaine Heredia, with whom she also starred in the 1999 film Flawless. In Rent she starred as Mimi Marquez, the HIV-positive, heroin-addicted nineteen-year-old who works at the Cat Scratch Club as an exotic dancer. Rubin-Vega did not participate in the film version of Rent with six of the stage version's original cast members due to her pregnancy at the time of the casting. The role was instead cast with Rosario Dawson, a newcomer to musicals. Rubin-Vega has been nominated for the prestigious Tony Award twice in her career so far: once for her role in Rent and again for her role as Conchita in Anna and the Tropics. She won the Theatre World Award in 1996 for Rent. She was also awarded the Blockbuster Award for Best Supporting Actress in a Suspense Thriller for her role in the film Wild Things with Kevin Bacon and Denise Richards. She also appeared in the 2000 production of The Rocky Horror Show.

Currently, Rubin-Vega is preparing for the release of her second full-length album of original songs titled Redemption Songs and slated for release in early 2006. Her rock band DRV are currently performing live shows in New York. She is also starring with Phylicia Rashad in a musical version of Federico Garcia Lorca's The House of Bernarda Alba at the Lincoln Center in March. She will soon be playing the role of Fantine in the 2006 revival Claude-Michel Schönberg popular musical Les Misérables - the original run of which is the third-longest running Broadway show, behind The Phantom of the Opera and Cats .