Bernthal was discovered by the executive director of Harvard University's Institute for Advanced Theater Training at the American Repertory Theater in Cambridge, Massachusetts, and graduated in 2002 from the American Repertory Theater with a Master of Fine Arts.

Since 2002, Bernthal has performed in over 30 plays regionally and Off-Broadway, including many with his own award-winning theatre company, Fovea Floods. He also had small guest roles in television series such as Boston Legal, CSI: Miami, and How I Met Your Mother. Bernthal booked his first regular role on a television series with the sitcom The Class, which was created by Friends co-creator David Crane. The show was cancelled after only one season. After this, he had roles in films such as World Trade Center and Day Zero.

In 2009, Bernthal had a supporting role in the Ben Stiller comedy film Night at the Museum: Battle of the Smithsonian as mobster Al Capone. The same year, he became a series regular on the television series Eastwick, which was cancelled after only one season.

In 2010, Bernthal portrayed Sgt. Manuel Rodriguez on the HBO miniseries The Pacific. Bernthal portrayed Shane Walsh in Frank Darabont's The Walking Dead, based on the comic book series of the same name. He was a regular on the show until 2012 and was nominated for the Breakout Performance – Male Award at the 2011 Scream Awards for his performance. That same year, he guest starred in an episode of NBC's legal comedy-drama series Harry's Law as Lucas Trassino. In 2013, he appeared in the crime drama film Snitch.

Bernthal reunited with Darabont for the TNT series Mob City, in which he portrayed Joe Teague, a police officer working in a corrupt 1940s Los Angeles, which was subsequently cancelled after one season. He also had supporting roles in the Martin Scorsese film The Wolf of Wall Street and the sports comedy film Grudge Match. He played southerner Grady "Coon-Ass" Travis in the 2014 World War II film Fury, opposite Brad Pitt, Shia LaBeouf, Michael Peña and Logan Lerman.

Bernthal appears as a playable character in the video game Call of Duty: Advanced Warfare in a downloadable game mode "Exo Zombies". Bernthal next co-starred in Denis Villeneuve's action drama film Sicario, opposite Emily Blunt and Josh Brolin, which won numerous awards and received positive reviews from critics.

In June 2015, Marvel announced that Bernthal would portray Frank Castle / The Punisher in the second season of Netflix's superhero series Daredevil, which was released on March 18, 2016. and is set to reprise the latter role in the Netflix series The Punisher.

In 2017, he appeared in Edgar Wright's Baby Driver, a crime comedy in which he played Griff. Also in 2017, he starred in Sicario writer Taylor Sheridan's directorial debut Wind River, which premiered at the 2017 Sundance Film Festival. In January 2019, Bernthal joined the cast of The Many Saints of Newark, the prequel feature film of HBO's The Sopranos. The film will be released in September 2021. During the beginning of 2019, Bernthal reprised his role in the film version of Small Engine Repair, a play in which he originated the role of Terrance Swaino in 2011. The film's release date has yet to be announced. In Summer 2019, Bernthal filmed Those Who Wish Me Dead, a western film directed by Taylor Sheridan who previously wrote Sicario, which featured Bernthal.

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