Neuwirth first met Bob Dylan in 1961, at the inaugural Indian Neck Folk Festival held in Branford, Connecticut. He soon became Dylan's friend and associate, as well as his road manager. Neuwirth consequently accompanied Dylan on his England tour in 1965, the Newport Folk Festival that same year that saw the Electric Dylan controversy, and featured alongside him in D. A. Pennebaker's documentary Dont Look Back (1967).
According to Neuwirth, Dylan planned to collaborate on a film with Warhol superstar Edie Sedgwick, who had signed with Dylan's manager, Albert Grossman. Neuwirth also took part in the Andy Warhol, Up-Tight multimedia event, which later evolved into the Exploding Plastic Inevitable. After Sedgwick left Warhol's circle, Neuwirth made a short "Chaplinesque, satirical movie" with her on Easter Sunday in 1966.
Neuwirth pulled back from Dylan's circle after the latter's motorcycle accident in 1966 and subsequent withdrawal from public life. However, he returned in time to help assemble the backing band for the Rolling Thunder Revue tour ten years later. He also appeared in Dylan's own self-referential romantic fantasy/tour film Renaldo and Clara (1978). The lower half of him appears behind Dylan in Daniel Kramer's front cover photo for the album Highway 61 Revisited.
With Janis Joplin and poet Michael McClure, Neuwirth co-wrote the song "Mercedes Benz" in August 1970, while improvising during a drinking session at a bar in Port Chester, New York. He scribbled the lyrics onto a napkin, which Joplin sang at her Capitol Theatre show that same night and then recorded a cappella just three days before she died. Neuwirth also introduced Kris Kristofferson to Joplin, who would have a major posthumous hit single with Kristofferson's song "Me and Bobby McGee", which Neuwirth first played for Joplin. Colin Irwin wrote:Painter, road manager, sidekick, confidante, henchman, poet, underground cult hero, womanizer, party organizer, self-appointed king of cool, and baiter-in-chief of Baez, Donovan, and any other unfortunate who wound up in the line of fire of his sledgehammer jibes, Neuwirth went on to become a film-maker and a credible singer-songwriter in his own right, co-writing the wonderful "Mercedes Benz" with his friend Janis Joplin.
After moving to Los Angeles during the 1970s, Neuwirth released his debut album Bob Neuwirth (1974) with Asylum Records. It included guest artists such as Kris Kristofferson, Booker T. Jones, Rita Coolidge, Chris Hillman, Cass Elliot, Dusty Springfield, Don Everly, Richie Furay, and Iain Matthews. It was not commercially successful, in part because he declined to publicize it extensively. The album eventually became a cult favorite and a proposal to reissue it was in place at the time of Neuwirth's death. Fourteen years later, he released his second album, , which was received more positively by critics. His third album, a collaboration with John Cale titled (1994), was described by The Daily Telegraph as "ambitious, experimental and doom-laden". While embarking on a national tour of the U.S., he recorded his fourth solo album, (1996), at the residences of friends such as Patti Smith, Bernie Leadon, and Elliott Murphy. He subsequently travelled to Havana to collaborate with José María Vitier on (1999), which was characterized as a wholehearted effort at fusion between folk and blues with Cuban music.