Arthur Edward Pepper Jr. was born on September 1, 1925, in Gardena, California. His mother was a 14-year-old runaway and his father a merchant seaman, both heavy drinkers, and as a small child he was sent to live with his paternal grandmother. He started on clarinet at nine and switched to alto saxophone at 13, and he was soon jamming on Central Avenue, the center of Black nightlife in Los Angeles. As a teenager he worked in Los Angeles bands led by Lee Young and Benny Carter, and by November 1943 he was playing alto in the orchestra of Stan Kenton, with which he is on a Los Angeles recording session that month. The war interrupted that start: he served in the U.S. Army, including a posting in London, and came back to Kenton in 1947. He stayed until 1952, in the second alto chair that served as the saxophone section's jazz seat, and is on Kenton's Capitol recordings through September 1951 alongside Bud Shank, Bob Cooper, Shorty Rogers, Maynard Ferguson and Shelly Manne.

Away from Kenton he began recording under his own name in 1952. A Lighthouse Café session led by Shorty Rogers on January 6, 1952 was followed on February 12 by two sets at the Surf Club in Hollywood with pianist Hampton Hawes, bassist Joe Mondragon and drummer Larry Bunker, the earliest recordings with Pepper as leader, and then by studio sides for what Savoy later issued as Surf Ride (1956), cut in 1952, 1953 and 1954 with Hawes, with Russ Freeman, and with Jack Montrose and Claude Williamson. A March 30, 1953 Lighthouse engagement with Sonny Clark produced live tapes that were first released in 1978. He finished second only to Charlie Parker among alto players in the 1952 DownBeat readers' poll. He had been addicted to heroin since the 1940s, and drug convictions interrupted his career for years at a time, with prison terms in 1954 to 1956, 1960 to 1961, 1961 to 1964 and 1964 to 1965.

The stretch between prison terms produced most of the recordings that made his name. Free again in 1956, he cut The Return of Art Pepper (August 6, 1956) with trumpeter Jack Sheldon, played in the Johnny Mandel-arranged band behind Hoagy Carmichael on Pacific Jazz that September, which included the song "Winter Moon," and took part in a big-band date for Chet Baker on October 26 and the sextet session Playboys with Baker on October 31. On January 19, 1957 he made Art Pepper Meets the Rhythm Section for Contemporary with Red Garland, Paul Chambers and Philly Joe Jones, the rhythm section of the Miles Davis quintet of the day. By Pepper's own telling he had never met them and learned of the session only that morning, and the album became a milestone of his career. In March to May 1959 he recorded Art Pepper + Eleven: Modern Jazz Classics in Marty Paich arrangements of bebop standards, with Pepper on alto, tenor and clarinet. Three more Contemporary dates followed in 1960: Gettin' Together! on February 29 with Wynton Kelly and Chambers and Jimmy Cobb, Smack Up on October 24 and 25 with Sheldon, and Intensity in November. The sleeve notes to the last two already hear him loosening up under the example of John Coltrane and Ornette Coleman. He then spent most of the next several years in prison, the last two terms at San Quentin, where he played in a group with saxophonist Frank Morgan, who was also serving a drug sentence.

After his release he played mostly tenor saxophone for a time, absorbing Coltrane's example. In 1968 he joined Buddy Rich's big band on alto and can be heard in its live album Mercy, Mercy from Caesars Palace in Las Vegas (July 7, 1968), and on November 24, 1968 he led a quintet with tenor saxophonist Joe Romano at Donte's in North Hollywood. From 1969 to 1971 he lived at Synanon, the drug-rehabilitation program that later became a cult. He began methadone therapy in the mid-1970s, and from April 1972 he began telling his life story to his wife Laurie Pepper, who recorded and edited the interviews over seven years into the autobiography Straight Life (1979). A concert at Foothill College on February 14, 1975 preceded the comeback album Living Legend, recorded on August 9, 1975 with Hampton Hawes, Charlie Haden and drummer Shelly Manne.

The last seven years were the most heavily documented of his career. For Contemporary he recorded The Trip in September 1976 with George Cables and Elvin Jones and No Limit in March 1977, made his Tokyo debut in April 1977 (the live album Tokyo Debut), and on July 28, 29 and 30, 1977 recorded at the Village Vanguard with Cables, bassist George Mraz and Jones, a residency that Contemporary issued as three albums plus a fourth volume. At Galaxy, a Fantasy Records label, he made Art Pepper Today (December 1978, with Stanley Cowell, Cecil McBee and Roy Haynes), Straight Life (September 21, 1979, with Tommy Flanagan, Red Mitchell and Billy Higgins), the Tokyo concert Landscape (July 16, 1979), and Winter Moon (September 1980), an album with strings arranged by Bill Holman and Jimmy Bond. Sessions with Hank Jones, Ron Carter and Al Foster on February 23, 1979 supplied So in Love and the later New York Album. In 1981 he toured Europe, recorded at the Maiden Voyage club in Los Angeles (August 13 and 15, 1981, issued as Roadgame, Art Lives and APQ), and on September 27 played a UCLA concert with Zoot Sims that Pablo released as Art 'n' Zoot. His last studio sessions were the duo albums Goin' Home and Tête-à-Tête with Cables in the spring of 1982. He died of a stroke in Los Angeles on June 15, 1982, at 56, and was interred at Hollywood Forever Cemetery. The documentary Art Pepper: Notes from a Jazz Survivor appeared in 1982, and Laurie Pepper's Widow's Taste label has issued his previously unreleased concert recordings since 2006.

Pepper was a lyrical, emotionally exposed alto player with a bright, pure tone and a precise way of stating even fast notes, and he built solos from broken phrases and shifting accents. Britannica ties his early manner to the swing altoist Benny Carter and to the bop players Charlie Parker and Lee Konitz, and as a West Coast figure he is usually grouped with Chet Baker, Gerry Mulligan and Shelly Manne, though his playing is hotter and more intense than the cool-school label suggests. By the 1960 sessions the example of John Coltrane and Ornette Coleman was loosening his phrasing, and in the 1970s he worked modal material, cyclic forms and dense, sheets-of-sound passages into his solos. He was also a strong ballad interpreter, and a composer whose originals such as "Straight Life," "Patricia" and "Las Cuevas de Mario" stayed in his sets. Critic Scott Yanow wrote that by the end of his life Pepper had realized his ambition of being regarded as the world's greatest altoist, and critics have ranked Straight Life among the best of the jazz autobiographies. He is closely identified with George Cables, his regular pianist for his last five years, and with his Contemporary albums of 1957 to 1960 and his Contemporary and Galaxy albums of the late 1970s.