Harris was born in Albuquerque, New Mexico on June 15, 1973. His parents, Ron and Sheila Harris, are both lawyers, and his mother is also a writer.

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As a fourteen-year-old, Harris attended a drama camp at New Mexico State University, where he met writer Mark Medoff, who was working on a project that became the film Clara's Heart (1988), directed by Robert Mulligan.

Soon Harris began his professional acting career with roles in Linda Shayne's Purple People Eater (1988) and Mulligan's Clara's Heart. His performance in the latter won him a Golden Globe nomination in the category of Supporting Actor.

In 1989 he became the star of the television "dramedy" series Doogie Howser, M.D., which was about a precocious youngster who had become a doctor at the age of fourteen. In the opening episode, sixteen-year-old Doogie interrupted the road test for his driver's license to attend to an accident victim.

The show continued to play on Doogie's dual identity as a skilled doctor and a typical teen. The former provided the drama in the series as Doogie demonstrated his professional expertise, winning the admiration of initially skeptical adult colleagues. The comedy derived largely from Doogie's social interactions with age-mates, especially his somewhat eccentric best friend, Vinnie, and his girlfriend, Wanda. The teen-age romance ended unhappily, however, as Doogie and Wanda broke up, but not before losing their virginity.

Harris garnered three Young Actor Awards as Best Young Actor Starring in a Television Series (1990-1992) and also earned a Golden Globe nomination for Best Performance by an Actor in a TV Series—Comedy/Musical in 1992.

When the highly successful series ended its run in 1993, Harris was firmly cemented in the minds of many viewers as the winsome Doogie, but he managed to get beyond that image by playing against type in several made-for-television movies and in Paul Verhoeven's theatrically released science fiction film Starship Troopers (1997), in which he portrayed a gung-ho military officer.

Harris also began working in the theater, appearing on stage as the narrator in a Los Angeles production of Jonathan Larson's Rent (1997). He briefly returned to television with a co-starring role in the situation comedy Stark Raving Mad (1999-2000), but the show was cancelled after only twenty-two episodes.

Harris debuted on Broadway in David Auburn's Proof in 2002, and the following year he stepped in as the Emcee in a production of Cabaret (book by Joe Masteroff, music by John Kander, lyrics by Fred Ebb).

His performance in Cabaret was especially well received, and he enjoyed the challenge of it, noting, "The whole idea of the Emcee's role is that he . . . defines transformation. He starts off very happy and charming as the 'Willkommen' man, and then he's an aristocrat flaunting his money, or a lovesick man falling in love for the first time. Sometimes he's a woman in a kick line. It's not until the final transformation at the end that you realize who he truly is."

Harris continued his work on Broadway in 2004, appearing in the double role of the Balladeer and Lee Harvey Oswald in Stephen Sondheim's Assassins. He returned to the big screen later that year with a small but much commented upon part in Danny Leiner's comedy Harold & Kumar Go to White Castle.

The credits for Harold & Kumar list his role as "Neil Patrick Harris" rather than as "Himself" since the character was nothing at all like the real Harris or his well-remembered image as Doogie. He also appeared in the 2008 sequel, Harold & Kumar Escape from Guantanamo Bay (directed by Jon Hurwitz and Hayden Schlossberg) as the same character, described by Donna Freydkin as "a doped-up, egomaniacal, prostitute-loving, unicorn-riding narcissist wielding his own personalized branding iron."