Dylan was born on December 9, 1969 in New York City to Bob Dylan and his wife Sara, both of whom are Jewish. The youngest of five children, Dylan spent the earliest years of his life in Greenwich Village. Around the age of three, he moved with his family to the Los Angeles area. Growing up, he listened to English rock records from his older brothers' record collection, including the Clash, the Jam and the Buzzcocks. Dylan was particularly impressed with the Clash, who inspired Dylan to begin playing music himself. During high school, Dylan played guitar in various bands; he was featured as a guitar player on his friends' band's eponymous 1987 album, Trash Matinee. Dylan was also in a band called the Bootheels at the time with Future Wallflowers bandmate Tobi Miller. It was during this time that Dylan started writing songs and began shifting his focus from guitar playing to songwriting. Upon graduation from high school, however, Dylan decided to move to New York City to attend Parsons School of Design to study art. Dylan subsequently dropped out in his first semester and moved back to Los Angeles to pursue music.

Dylan married his girlfriend Paige, a Screenwriter, in 1992. The couple have four sons together and live in Los Angeles.

Upon return from a tour in 1993, the band learned that management at Virgin had shifted, leading to the removal of Jeff Ayeroff and Jordan Harris, who had signed the Wallflowers to the label. The new executives at Virgin were not pleased with the Wallflowers' slow sales and the band did not feel they had a Future with the label, so they asked to be released from their contract; Virgin complied and by the end of the year, the Wallflowers were left without a label. The band went back to playing clubs in Los Angeles and looking for a new label. During this time, the band went through a number of personnel changes. In 1993, Maguire was asked to leave for undisclosed reasons. However, the band would continue playing shows with another bass player, Jimmie Snider, until May 1993, when the band found a permanent replacement. Greg Richling, whom Dylan went to high school with, became the band's new Bassist. Richling remained a member of the Wallflowers for the next two decades, until he left in 2013. The band continued to play club shows in Los Angeles through mid-1994; it was around this time when Yanowitz left the Wallflowers to join 10,000 Maniacs, then fronted by his girlfriend, Natalie Merchant. Shortly after Yanowitz's departure, the Wallflowers caught the attention of Tom Whalley and Jimmy Iovine of Interscope Records, who signed the band in 1995.

The Wallflowers began recording their second album, Bringing Down the Horse in 1995. Around the time they began recording, however, founding member Tobi Miller left the band. A number of guitarists stepped in to finish the album. Bringing Down the Horse was produced by T Bone Burnett and the songs were written by Dylan. The album was released on May 21, 1996. To promote the release, the band toured extensively through the rest of 1996 and through 1997. The Wallflowers now included Drummer, Mario Calire and Guitarist Michael Ward, in addition to Dylan, Jaffee and Richling. The band performed shows as headliners, as well as openers for acts such as Sheryl Crow in early 1997 and Counting Crows in the summer of 1997. They also opened for Tom Petty and the Heartbreakers in January 1997, as well as for the Rolling Stones and Bob Dylan in November 1997. In June 1997 Dylan was featured on the cover of Rolling Stone. In the issue's accompanying interview, Dylan spoke at length about his lineage for the first time.

The Wallflowers entered the studio towards the end of 1999 with producers Michael Penn and Andrew Slater, the Wallflowers' manager. (Breach) took about eight months to record and was released on October 10, 2000. The Wallflowers embarked on a tour that lasted through the end of 2000 and into 2001, making stops in Japan and Madison Square Garden in New York for a four-night run, opening for the Who. In October 2000, Dylan was featured on the cover of Rolling Stone for a second time. In October 2001, Guitarist Michael Ward announced he was leaving the Wallflowers, citing creative differences.

Dylan began writing for the Wallflowers' fourth album, Red Letter Days in 2001. The band recorded demos while on tour with John Mellencamp that year before getting into the studio in Santa Monica, California. Due to the absence of a lead Guitarist during the recording for Red Letter Days, Dylan took on more lead guitar duties than he had previously. Red Letter Days was produced by founding Wallflowers member Tobi Miller and Bill Appleberry. Following the release of the album's first single, "When You're On Top" on August 16, 2002, Red Letter Days was released on November 5, 2002. Following tours in the U.S. and Europe, Drummer Mario Calire announced he was leaving the Wallflowers in 2003.

In 2005, Dylan spoke about his relationship with his father for the first time in an interview with The New York Times. Due to the fact that Dylan rarely speaks about his father, there have been ongoing rumors that their relationship is strained. Dylan rebuffed these claims, speaking of his father as "affectionate" towards him and went on to say the two have a "great relationship."

Beginning in 2006, Dylan began playing shows without the Wallflowers, though he did tour with the band on numerous occasions between 2007 and 2009. In May and June 2006, Dylan toured with former Wallflowers Producer T Bone Burnett, performing solo acoustic opening sets. In fall of that year, Dylan's song "Here Comes Now" was featured as the theme song for an ABC drama, Six Degrees. Also in the fall of 2006, it was announced that Dylan had signed a solo recording contract with Columbia Records.

In September 2007, it was reported by The New York Times that Dylan was recording his first solo album at Producer, Rick Rubin's home in the Hollywood Hills. Regarding its sparse instrumentation and production, Dylan described the differences in the writing process for Seeing Things, compared to writing for the Wallflowers:

Following the completion of recording in 2007, Seeing Things was released on June 10, 2008. The album received generally favorable reviews and peaked at No.24 in the U.S. on the Billboard 200. Following the release of Seeing Things, Dylan made several television appearances to promote the album and toured with a backing band called the Gold Mountain Rebels, which consisted of Wallflowers Drummer Fred Eltringham, Guitarist Audley Freed and Bassist George Reif. In the summer and fall of 2008, Dylan and the Gold Mountain Rebels played a combination of theaters and festivals in the U.S., Europe, and Japan, including Farm Aid in Mansfield, Massachusetts and the Newport Folk Festival. In addition to touring with the Gold Mountain Rebels, Dylan and Eltringham also performed several shows with the Wallflowers in 2008.

In 2009, Dylan visited T Bone Burnett at a studio where Burnett was producing the Soundtrack for the film Crazy Heart. Burnett asked Dylan if he had any new songs to show him. The only song Dylan had was one he'd written for Glen Campbell's forthcoming album, Ghost on the Canvas, called "Nothing But the Whole Wide World." Burnett was impressed by the song and asked Dylan to come up with fifteen additional songs so they could put an album together. Dylan came back to Burnett six weeks later with the songs and in 2009 they recorded Dylan's second solo album, Women + Country.

Also in 2010, Dylan sang backing vocals on the Court Yard Hounds' song "See You In the Spring." Along with being released on the Court Yard Hounds' eponymous debut album, the song was specially released as a 45 RPM single for Record Store Day, 2010. Dylan's song "Everybody's Hurting" from Women + Country was featured as the B-side to the record.

In May 2011, Dylan was awarded an honorary Doctor of Letters degree from Idaho State University.

The Wallflowers recorded their sixth studio album, Glad All Over in Nashville, Tennessee in early 2012. Shortly before entering the studio, the band replaced Drummer Fred Eltringham with Jack Irons. The writing process was different for this album than previous Wallflowers albums; instead of Dylan bringing in completed songs, he brought only lyrics to the studio and as a band, they wrote the music for the songs. The Wallflowers toured throughout the summer and fall of 2012. Glad All Over was released on October 9, 2012 on Columbia Records. In the spring of 2013, the Wallflowers did an arena tour opening for Eric Clapton.

Aside from work with the Wallflowers, Dylan has played a key role of several other projects recently. In early 2013 Dylan, along with Dave Matthews, Charlie Sexton, Brady Blade, and Sexton's brother Will, wrote and recorded an album in Shreveport, Louisiana as a new band called the Nauts. The album has yet to be released. In September 2015, Dylan released a duet online with Cat Power covering the Turtles' "You Showed Me." It was announced that the song would be part of a forthcoming studio album called Echo in the Canyon where Dylan would cover songs in duets by 1960's-era Southern California folk rock artists such as the Turtles, the Mamas & the Papas, Buffalo Springfield, and the Beach Boys. It was also announced that Dylan, along with Regina Spektor, Cat Power, Beck, Fiona Apple, and Jade Castrinos, would be performing these songs in concert at the Orpheum Theatre in Los Angeles in October 2015. The Echo In The Canyon album does not yet have an official release date but is expected to be released by the end of 2017 and will by accompanied by a documentary about the project.

Dylan is a supporter of diabetes awareness and was given a Father of the Year award from the American Diabetes Association on June 4, 2014. The award recognizes, "men that have made family a priority, while balancing a demanding career and community involvement." Dylan is also a supporter of Crohn's and colitis awareness. Each year since 2012 he has provided musical entertainment for an annual event put on by Connecting to Cure, a nonprofit dedicated to promoting awareness and funding research to cure Crohn's and colitis.