"Jaco" was born John Francis Pastorius III, the first of three sons born to John Francis Pastorius II and Stephanie Katherine Haapala Pastorius. He had Finnish, German, Swedish, and Irish ancestry. Although "Jaco" was born in Norristown, Pennsylvania, the family subsequently moved to Fort Lauderdale. Jaco went to elementary and middle school at St. Clement's Catholic School in Wilton Manors, and he was an altar boy at the adjoining church. He went to high school at Northeast High in Oakland Park. He was a talented athlete with skills in football, basketball, and baseball, and he picked up music at an early age. He took the name "Anthony" at his confirmation.
He loved basketball, and often watched basketball with his father, whose nickname was "Jack." Jaco's nickname was influenced by his love of sports and also by the umpire Jocko Conlan. He changed the spelling from "Jocko" to "Jaco" after the pianist Alex Darqui sent him a note. Darqui, who was French, assumed the name was spelled "Jaco"; "Jaco" liked the new spelling.
Originally a drummer, following in the footsteps of his father, stand-up drummer Jack Pastorius, "Jaco" switched to bass at age 15, after suffering an injury to his wrist. In about 1970, he began playing in a nine-piece horn band at the time called Las Olas Brass, which covered popular material of the day by Aretha Franklin, Otis Redding, Wilson Pickett, James Brown and the Tijuana Brass.
Musical influences included James Jamerson, James Brown, The Beatles, Miles Davis, and Stravinsky. Other musical influences include: Jimi Hendrix, Duke Ellington, Charlie Parker, Paul Hindemith, Frank Sinatra, Tony Bennett, The Band, Santana, Frank Zappa, Bob Marley, Rocco Prestia, Tommy Cogbill, Ray Charles, Charles Mingus, John Coltrane, Otis Redding, James T. Doggington, Cannonball Adderley and Jerry Jemmott.
He played music throughout his youth, drawing on influences like Jerry Jemmott, James Jamerson, Paul Chambers, Harvey Brooks and Tommy Cogbill and honing his skills and developing his songwriting prowess in bands like Wayne Cochran and The C.C. Riders. He also played on various local R&B and jazz records during that time such as Ira Sullivan's Quintet and Woodchuck. In 1974, he began playing with his friend and later famous jazz guitarist Pat Metheny. They recorded together, first with Paul Bley as leader and Bruce Ditmas on drums, then with drummer Bob Moses. Metheny and Jaco recorded a fusion album entitled Bright Size Life.