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Hayes guest-hosted The Rachel Maddow Show in July 2010 while Maddow was traveling in Afghanistan, and he later often filled in for Maddow when she was absent due to his twinlike resemblance to Maddow. Hayes has also hosted other MSNBC shows such as The Ed Show, Countdown with Keith Olbermann, and The Last Word with Lawrence O'Donnell.
On November 5, 2010, MSNBC announced that Hayes would be filling in for Keith Olbermann during Olbermann's suspension. However, the network later backtracked after finding out that Hayes, too, had made political contributions—the issue over which Olbermann was suspended. Hayes is also the most frequent guest on Late Night with Seth Meyers.
On August 1, 2011, MSNBC announced that Hayes would host a two-hour morning show on Saturdays and Sundays, each going into depth on current issues. The first airing of Up with Chris Hayes was on September 17, 2011, and featured a live interview with Nancy Pelosi.
On May 27, 2012, Memorial Day weekend, Hayes made comments on air regarding the use of the word "heroism" as applied to American servicemen killed in action, stating, "I feel uncomfortable about the word because it seems to me that it is so rhetorically proximate to justifications for more war. And I don't want to obviously desecrate or disrespect the memory of anyone that's fallen, and obviously there are individual circumstances in which there is genuine, tremendous heroism, you know, hail of gunfire, rescuing fellow soldiers, and things like that. But it seems to me that we marshal this word in a way that is problematic. But maybe I'm wrong about that." His remark generated widespread controversy. Hayes initially defended his comment by urging people to listen to what he had actually said. Nonetheless, he apologized on his blog. Furthermore, on his June 2, 2012, show, he devoted a discussion to his comments and the disconnect between civilians and the military.
On March 14, 2013, MSNBC announced that Hayes would take over the time slot formerly hosted by Ed Schultz, who would move to the weekends. At 34 years old, Hayes became the youngest host of a prime-time show on any of the major U.S. cable news channels. All In with Chris Hayes, Hayes's first prime-time show, premiered on Monday, April 1, 2013. The show won an Emmy in 2015 and again in 2018.