Ferrer was born in Santa Monica, California, the oldest of five children of Academy Award winning actor José Ferrer and singer Rosemary Clooney. His father was Puerto Rican, while his mother had English, German, and Irish ancestry. Ferrer siblings were sisters, Maria and Monsita, and brothers, Gabriel (later the husband of singer Debby Boone) and actor Rafael. He was the cousin of actor George Clooney and the nephew of journalist Nick Clooney. Ferrer was raised in Hollywood, California; as a teenager, his interests shifted toward music. He played the drums on Keith Moon's Two Sides of the Moon.
Ferrer's friend, Bill Mumy cast him as a drummer in the series Sunshine, his first television role. Ferrer was also Mumy's bandmate in Seduction of the Innocent, a band that also consisted of Steve Leialoha, and Max Allan Collins.
Ferrer began his career in the early 1980s making guest appearances on episodic television. He played the younger self of his father's character on Magnum P.I in 1981. In 1983, he was given a small part as a waiter in The Man Who Wasn't There. He also had a minor role in Star Trek III: The Search for Spock (1984) as the U.S.S Excelsior helm officer. He had a major role in the 1987 action movie RoboCop as aspiring, cocaine-snorting corporate executive Bob Morton. After appearing as Morton. Ferrer's notable later roles include a sinister biker in Valentino Returns, an overzealous engineer in DeepStar Six (1989), a resourceful vigilante in Revenge (1990), Commander Arvid Harbinger in the comedy Hot Shots! Part Deux (1993), Lloyd Henreid in the Stephen King miniseries The Stand (1994), and a drug informant in Traffic (2000). He occasionally took on lead parts as well, such as The Harvest and The Night Flier.
In the early 1990s, Ferrer appeared on three primetime TV series simultaneously: as D.A. Todd Spurrier in Shannon's Deal (1989–1991), as Cajun cop Beau Jack Bowman in Broken Badges (1990–1991), and as cynical, wittily abrasive FBI forensics specialist Albert Rosenfield in Twin Peaks (1990–91). Ferrer reprised the role of Rosenfield in the movie Twin Peaks: Fire Walk with Me (1992). Ferrer played a super-villain called "The Weatherman" in the failed 1997 TV pilot, Justice League of America. Later in the same year, he provided the voice for a similar character, the Weather Wizard, in the Superman: The Animated Series episode "Speed Demons". In 1999, Ferrer voiced Aquaman in another Superman: Animated episode, "A Fish Story". The same year, at the 41st Grammy Awards, Ferrer was nominated for "Best Spoken Word Album for Children" in Disney's The Lion King II, "Simba's Pride Read-Along".
Ferrer again played a medical examiner on the small screen, Dr. Garret Macy, in the television crime/drama series Crossing Jordan (2001–07). In 2003, Ferrer made his New York stage debut in the off-Broadway production of The Exonerated. In 2004, Ferrer performed as the voice of the Heretic leader in the video game Halo 2. Ferrer took voice-over roles in the TV series Robot Chicken (2006) and American Dad! (2007). He played Jonas Bledsoe on NBC's Bionic Woman series and in 2009 also starred in another NBC series, Kings, as a military commander of Gath.
Ferrer played Los Angeles Police Lieutenant Felix Valdez in the 2011 Lifetime police procedural drama, The Protector. Also in 2011, he started a multiple-episode guest role on the final season of Desperate Housewives. Signed to a recurring role in NCIS: Los Angeles as Naval Criminal Investigative Service Assistant Director Owen Granger, Ferrer was promoted to a series regular for the fifth season on February 6, 2013. He also appeared in the 2013 film Iron Man 3 as the Vice President. Ferrer reprised his role of Albert Rosenfield in the 2017 revival of Twin Peaks.
Ferrer died on January 19, 2017, from throat cancer at his Los Angeles home at the age of 61.
Miguel O'Hara, the alter ego of the Marvel Comics superhero Spider-Man 2099, was named after Ferrer by Ferrer's friend, writer Peter David, who co-created the character.