Gibbard was born in Bremerton, Washington, where he spent his formative years, during the time of the grunge music explosion in the early 1990s. He graduated from Olympic High School in 1994. He also cites Jack Kerouac as a major influence. He studied engineering at Western Washington University. He was raised Roman Catholic and referred to himself as "this indoctrinated Catholic even though I haven't been to church of my own volition in 10 or 15 years now." In a 2003 interview Gibbard stated that while he had previously been a vegan, he had recently become a pescetarian.

While performing guitar in the band Pinwheel, Gibbard recorded a demo cassette under the moniker Death Cab for Cutie, titled You Can Play These Songs with Chords (1997). After receiving a positive response to the material, Gibbard expanded the project into a full band, with the addition of Chris Walla (guitar), Nick Harmer (bass) and Nathan Good (drums). The following year, the band released its debut album, Something About Airplanes (1998), on Barsuk Records, and released its follow-up, We Have the Facts and We're Voting Yes, in 2000.

In addition, Gibbard, alongside Steve Fisk, composed and recorded the score for AJ Schnack's 2006 documentary, Kurt Cobain: About a Son. The film also features his cover of Beat Happening's "Indian Summer".

He had a small role in the John Krasinski film Brief Interviews with Hideous Men based on the David Foster Wallace short story collection of the same title. He completed a solo tour through the US in the spring of 2007 that featured David Bazan of Pedro the Lion and singer-songwriter Johnathan Rice.

He reportedly gave up alcohol in 2008 and began running marathons. He ran his first trail ultra-marathon (a running race longer than 26.2 miles) in 2013 and since then has completed several each year.

Gibbard became engaged to Actress and musician Zooey Deschanel in 2008. The couple married in September 2009 near Seattle, Washington. They announced their separation on November 1, 2011. Deschanel filed for divorce on December 27, 2011, citing irreconcilable differences. The divorce became final on December 12, 2012. Gibbard married Photographer and tour manager Rachel Demy on October 21, 2016 in Seattle, Washington.

Gibbard is the subject of the song, "Ben's My Friend", by indie folk act Sun Kil Moon. The track appears on the project's sixth studio album, Benji (2014). On Sun Kil Moon's follow-up album, Universal Themes (2015), primary recording Artist Mark Kozelek again refers to his friendship with Gibbard on its closing track, "This Is My First Day and I'm Indian and I Work at a Gas Station". Gibbard previously made a guest appearance on the band's third studio album, April (2008).

As of May 2015, Gibbard tours with four modified 1970s Fender Mustang guitars. Additionally he uses two custom-built Acme Silvertone amplifier heads. For use on acoustic songs he relies on two 2008 Gibson J-45 Acoustic Guitars with B-Band pickup systems. In the past, Gibbard used Fender Telecasters and G&L ASAT guitars.

Gibbard is an agnostic, lapsed Catholic: "I don’t want to falsely believe in something solely so I can jump to the front of the line for whatever this awesome place is we go after we die. [...] The vastness of that idea is so beyond my comprehension that I feel like if there was a God, then that God would accept me saying I’m not able to believe because it’s so outside of my ability to understand it. I understand that’s where faith comes into play."