There is conflicting information about Penn's age at the time of death, with some obituaries giving 1962 as his year of birth. In Richard T. Kelly's book, Sean Penn: His Life and Times (2004), Penn's mother indicated that his date of birth was October 10, 1965.

Penn started acting at the age of 12 at the Loft Studio and made his film debut in 1979’s Charlie and the Talking Buzzard, starring Christopher Hanks. In 1983, he was featured in Francis Ford Coppola’s youth drama Rumble Fish and appeared in the high school football drama All the Right Moves as the best friend of Tom Cruise's character. He also appeared in the hit dance movie Footloose in 1984 as the best friend of Kevin Bacon's character; played a villain in the Clint Eastwood western Pale Rider (1985); and co-starred with his brother Sean Penn and mother Eileen Ryan in At Close Range (1986).

Penn, who had a black belt in karate, appeared in the 1989 motion picture Best of the Best as Travis Brickley, a cocky member of the U.S. Taekwondo team taking on the team from Korea. The film also starred James Earl Jones, Sally Kirkland, Eric Roberts, Phillip Rhee, and Simon Rhee. Penn reprised his role in 1993's Best of the Best 2.

In 1990, Chris was cast in a season one episode of The Young Riders. He appeared as a villain and was killed by Josh Brolin's character william Hickok. In Robert Altman's 1993 ensemble film Short Cuts, Penn played a troubled swimming pool cleaner who is disturbed by his wife's profession (a telephone sex worker who takes calls from clients at home) to which Penn's character is sometimes obliged to Listen. He also appeared as a fall guy in a Criminal conspiracy in Murder by Numbers, alongside Sandra Bullock. Penn appears in Jay-Z's "Can I Get A..." 1998 music video as a bartender who mixes drinks and dances. He is also known for playing the character Clyde Cod in the 1998 film Rush Hour.

Two of his more memorable performances were in Reservoir Dogs as Nice Guy Eddie and True Romance as Nicky Dimes (both characters in scripts written by Quentin Tarantino). In 1996 he won the award for Best Supporting Actor at the Venice Film Festival for The Funeral.

In 2001, Penn was meant to appear in American Pie 2 as Steve Stifler's father, but the scenes featuring him were eventually cut as there was insufficient time to include him in the film's plot. However, they appeared on the deleted scene reel from the movie's DVD. Penn then went on to co-star opposite Peter Berg as the mafia brothers of Corky in Corky Romano. In 2003, he appeared on the Will & Grace episode, "Fanilow", as Barry Manilow's tour Director and a character who is interested romantically in Will. Penn was featured in an episode of the television crime drama Law & Order: Criminal Intent ("Death Roe") during the 2004–2005 season. He was also featured on the 2004 video game Grand Theft Auto: San Andreas as the voice of Officer Eddie Pulaski. Penn played himself on a 2005 episode of the HBO series Entourage. He appeared in The Darwin Awards, which premiered at the Sundance Film Festival one day after his death.

Penn was found dead in his Santa Monica condominium on January 24, 2006, aged 40. Although Penn had used drugs in the past, an autopsy performed by a Los Angeles County medical examiner revealed the primary cause of death was heart disease, with the prescription drug promethazine with codeine and an enlarged heart due to obesity being possible contributing circumstances. The toxicology report revealed that valium, morphine, marijuana and an elevated level of codeine were found in his bloodstream. Penn appeared slim and fit throughout the 1980s in movies such as Footloose, At Close Range and Pale Rider, but gained considerable weight throughout the 1990s. Sean Penn has said publicly in a TV interview on Larry King Live that his brother probably died because of his weight.