Muniz was born in Wood-Ridge, New Jersey, the son of Denise and Francisco Muniz III, a restaurant manager from Puerto Rico. Muniz was first discovered at age eight at a talent show in the Raleigh, North Carolina living in Knightdale (shortly after the family moved from Wood-Ridge), where he was cast as Tiny Tim in a local production of A Christmas Carol. His parents divorced shortly after. Muniz subsequently moved to San Diego, California with his mother and sister. He appeared in commercials and made his film debut in the made-for-television movie, To Dance With Olivia (1997), starring Lou Gossett Jr. The same year, he appeared in the CBS Hallmark Hall of Fame presentation of What the Deaf Man Heard. A small role in the film Lost & Found (1999) led up to his breakthrough role as the title character on Malcolm in the Middle, which would make him a familiar face in millions of households.

Fox premiered Malcolm in the Middle on January 9, 2000, as a mid-season replacement, and the show was quickly swamped with accolades. The premiere episode was watched by 23 million people; and the second episode by 26 million. Muniz then won many awards for the series, including young star awards, young artist awards and kids' choice awards. Muniz anchored the show with his narration and central role in many of the series' plots, although he has said that he does not consider himself a comic actor and does not find himself funny. He was nominated for Golden Globes in 2000 and 2001, the Emmy Awards in 2001, and was honored with the Hollywood Reporter 'Young Star Award' for his work in the series.

In April 2006, Muniz began filming My Sexiest Year, an independent film which will be shot in New York City and Miami, and which will star Oscar nominee Harvey Keitel as Muniz' father. Muniz' character will have a love scene in the film. The same month, Muniz announced he was taking a break from acting to pursue a career in race car driving, with a full-time two year racing deal with Jensen Motorsport in the Formula BMW competition, saying: 'Truthfully, I think it will be easier for me to leave for a while and come back to acting when I'm 23, 24 and be an adult and start fresh'. In May 2006, despite his announcement to temporarily leave acting, Muniz signed on to star in the raunchy teen sex comedy Parental Guidance Suggested, which will be rated R. The film was originally planned to be released in 2007 by Dimension Films. In late 2007, he made a significant guest appearance in an episode of the popular and critically acclaimed CBS crime drama, Criminal Minds. The episode, entitled "True Night", featured Muniz playing a famous comic book writer who becomes a violent serial killer that preys on a group of local gang-bangers after they force him to watch while they rape and murder his pregnant fiancee. In December 2007 he made a cameo appearance in the movie Walk Hard: The Dewey Cox Story.

Muniz already finished the movies Parental Guidance Suggested and My Sexiest Year, and will be out on DVD in 2008. Muniz also made the voice of Manu in the movie The Legend of Secret Pass which will also be out in 2008 in DVD release. Muniz has now stated that he resides in New York in a skyrise apartment. When asked why he stated "it's bangin yo, i can see all the fit birds from here init!".

Muniz started writing in 2004, when he wrote the screenplay of the TV movie Granted. To date, that is his only screenplay. In 2004, he was the executive producer of the movie Granted. In 2006, he also executive produced the movie Choose Your Own Adventure: The Abominable Snowman. A year later (2007) he became the associated producer of the film Choose Conn

Muniz's career in racing traces back to 2005, when he won the Toyota Pro/Celebrity Race as a celebrity participant. While investigating the possibility of joining a racing team as an owner, Muniz was granted a test in a car and instead signed a two year deal with Jensen Motorsport as a driver. In January of 2007, he placed second at the Sebring Winter National SCCA race