A high school dropout, Bouchard was working as a bartender in 1993 when he bumped into a former grade school Teacher of his, Tom Snyder, who asked if Bouchard was still drawing, and offered Bouchard a chance to work on a few animated short films Snyder was making. The shorts developed into Bouchard's first series, Dr. Katz, Professional Therapist, which he produced. He credits Jonathan Katz, H. Jon Benjamin, and Snyder as major influences. Dr. Katz ran for six seasons, from 1995 to 2000. He also produced one season of Science Court, another animated show made by Soup2Nuts.
Towards the end of Dr. Katz, Bouchard and Brendon Small teamed up to create Home Movies. The show was picked up initially by UPN, which dropped it after five episodes; the remaining eight episodes from season one, and the subsequent three seasons, were shown on Adult Swim. The show was not renewed after the conclusion of the fourth season in 2004.
After Home Movies concluded and another Bouchard pilot, Saddle Rash, was not picked up, Bouchard created Lucy, the Daughter of the Devil. The show's pilot was created on October 30, 2005, but it was not until September 2007 that the show debuted as a weekly feature on Adult Swim. He was a consulting Producer on HBO's The Ricky Gervais Show.
Bouchard lives in Los Angeles with his wife, Holly Kretschmar. The couple married on September 3, 2006.
In 2009, Bouchard got together with King of the Hill Writer and Producer Jim Dauterive and developed Bob's Burgers, an animated series about a family working at a hamburger restaurant. Bouchard grew up in a working-class family full of "blue collar creatives" and created Bob's Burgers because he didn't see that kind of life represented on TV. In 2010, Fox placed the series on the primetime slate for the 2010–11 television season. A special preview aired on Thanksgiving on November 25, 2010. When the series premiered, it received mixed reviews with a Metacritic score of 54 out of 100. However, as the first season progressed and concluded and the second began, critics began giving the series praise. The show has generally been viewed as a spiritual successor to King of the Hill, which carried less emphasis on shock comedy and focused more on character-driven humor. A film adaptation based on the animated TV series is in the works and is scheduled for a July 17, 2020 release.