By Keach Hagey and Joe Flint 

Jon Stewart, the comedian whose fake newscasts were at times more trusted by his young audience than the real ones they satirized, will step down as the host of "The Daily Show" this year after a 16-year run that helped reshape late-night television.

Mr. Stewart--who inherited "The Daily Show" after Craig Kilborn left it for a late-night show on CBS--did not invent the fake news format. But he did elevate it to an unprecedented level of cultural relevance, lampooning political figures and skewering the media with trademark montages taken from the day's news. He often also used his platform to conduct serious and at times probing interviews with major newsmakers.

Shortly after he sat down with the hosts of CNN's original version of "Crossfire," Tucker Carlson and Paul Begala, in 2004 and begged them to "stop hurting America" with their partisan yelling match, the show was canceled. A 2007 Pew Research Center Study found Mr. Stewart was tied in its rankings of most trusted journalists with Brian Williams, Tom Brokaw, Dan Rather and Anderson Cooper.

"This show doesn't deserve an even slightly restless host, and neither do you," a visibly emotional Mr. Stewart told viewers at the end of his program on Tuesday night. "It's been the honor of my professional life."

Mr. Stewart said he had "a lot of ideas" about what he wanted to do next, starting with having dinner with his family on a school night, "who, I have heard from multiple sources, are lovely people."

"Through his unique voice and vision, 'The Daily Show' has become a cultural touchstone for millions of fans and an unparalleled platform for political comedy that will endure for years to come," said Comedy Central President Michele Ganeless in a statement on Tuesday evening. "He is a comic genius, generous with his time and talent, and will always be a part of the Comedy Central family."

Mr. Stewart's contract is set to expire in September, and negotiations on the exact timing of his departure from the show are still under way, Mr. Stewart said.

Speculation about Mr. Stewart's ambitions beyond "The Daily Show" have been rampant since 2013, when Mr. Stewart took a leave of absence from his hosting duties to direct the 2014 film "Rosewater," about a journalist imprisoned in Iran whose satirical interview with "The Daily Show" is used as evidence against him.

Mr. Stewart's departure will follow that of Comedy Central's other high-profile late-night comic, Stephen Colbert. Mr. Colbert ended his program, "The Colbert Report," late last year and will launch a late-night talk show on CBS in 2015.

The loss of top talent at Comedy Central poses challenges for the channel's parent, Viacom Inc., which is already trying to rebound from sharp ratings declines across its biggest networks such as Nickelodeon, MTV and Comedy Central.

After Mr. Colbert's departure, the network created a show for "Larry Wilmore," who was known as the "senior black correspondent" on "The Daily Show." Mr. Wilmore's program, "The Nightly Show," premiered last month.

"The Daily Show" also proved to be an excellent springboard for several members of his team who became stars in their own right, including Mr. Colbert, Steve Carell and John Oliver. Mr. Oliver now hosts a show on Time Warner Inc.'s HBO.

"The Daily Show" has always drawn a relatively small but influential audience in the world of late night, averaging 2.1 million total viewers so far this season, according to Nielsen. But the show has always been highly attractive to advertisers for its ability to consistently pull in the elusive young male audience in the 18-34 demographic.

However, the arrival of Jimmy Fallon at the "Tonight" show on NBC has upset this steady state of affairs of late. While last season, "The Daily Show" was the clear winner among all viewers in the 18-34 demographic with 629,000 viewers by this point in the season, this year it has seen that demographic drop off by 22% so far this season, while Mr. Fallon's "Tonight" has pulled ahead--up 36%--to 519,000 viewers in that demographic. NBC, as a broadcast network rather than a cable network, has always drawn a bigger audience of total viewers, averaging nearly 4 million so far this season, according to Nielsen.

Write to Keach Hagey at keach.hagey@wsj.com and Joe Flint at joe.flint@wsj.com

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