Zucker, the company's CEO, told employees of his planned departure in an e-mail he sent Friday, a day after he set terms of his exit deal.
The possible change-in-command had been looming since last December when Comcast Corp. agreed to buy a 51 percent stake in NBC Universal from General Electric Co. That deal still hasn't cleared regulatory hurdles, but that is expected around the end of the year.
Zucker said it was becoming clear over the past few months that an exit is looming, and that he understood companies like to put in their own management teams in such takeovers. Two weeks ago, Comcast's chief operating officer, Steve Burke, told Zucker that a change would be made when the deal was complete.
"I had already gotten comfortable with that idea," he said. "I did not want to be a guest in my own house."
While NBC's news division and late-night programming has remained strong, Zucker presided over the downfall of NBC's prime-time lineup from its 1990s dominance in the "Friends" era to its past few years as a struggling fourth-place network.
He contends that NBC's entertainment troubles gets a disproportionate amount of attention given NBC Universal's success with cable networks. NBC Universal owns the NBC and Telemundo television networks along with 26 TV stations; cable channels USA, Bravo, Oxygen, Syfy, CNBC and others; the Universal Pictures movie studio and Focus Features; theme parks in California, Florida and Japan; and has part ownership of online video site Hulu.
"You've got to give us credit for the other stuff and, by the way, the other stuff is far more important financially," he said.
In the most recent quarter through June, financial results improved at the company mostly because of a rebound in advertising. Operating profit grew 13 percent to $607 million, with advertising, an improving performance by movies and theme park sales responsible.
Zucker's contract had been renewed last year to run through January 2013 with an annual salary of $6.3 million and a guaranteed annual bonus of $1.5 million. If he leaves by January, he can expect at least a $15.6 million check.
General Electric CEO Jeff Immelt said in a note to some GE leaders on Tuesday that Zucker has been "creative and composed" during turbulent times.
"Jeff has been a tough-minded, inclusive and innovative leader of NBC Universal," Immelt wrote. "He has always stepped up when the company needed him. He never blinked when it came to tough decisions."
NBC's experiment last season putting Jay Leno in prime time proved a spectacular failure, blowing up further when Conan O'Brien refused to move to a later time slot to accommodate Leno's return to late night. The Winter Olympics in Vancouver last year, while a ratings winner for NBC, cost the company a $223 million loss because rights negotiations were concluded in a different economic climate.
His inability to turn around NBC entertainment remains his biggest regret, he said. But after one week of the season, and a strong start for the much-hyped "The Event," Zucker said he sees "the seeds of a turnaround being planted."
Miller Tabak analyst David Joyce said Zucker's departure was expected because of the active role of Burke, a former ABC executive. While Joyce didn't see NBCU's performance as a reason for removing Zucker, "one could question who was responsible for the NBC network's ratings slippage over time."
Zucker, 45, was an NBC wunderkind who started at the company in 1986 as a researcher for its Olympics coverage. He moved to the "Today" show in 1989 and became its executive producer at age 26. The show dominated in the ratings behind Katie Couric, Bryant Gumbel and Matt Lauer, becoming hugely profitable for the company.
In an unexpected move, Zucker was sent to Hollywood to oversee NBC's entertainment division. He alienated many in California with his brash confidence and efforts to cut costs, and NBC is still mending fences with the creative community there. Still, he remained a favorite of G.E. executives, who continued to move him up the company's corporate ladder.
Zucker, in his e-mail, recalled the first day coming to work at NBC in August 1986. "It was humid and my shirt was soaking by the time I got there," he said. Zucker survived two bouts of cancer while at the "Today" show.
"Sure, there have been ups and downs in the last quarter century," he said in his e-mail. "But when I step back and think about what we've been through, I feel nothing but pride and joy. It has been a great run and I've been incredibly fortunate."
Brian Roberts, chairman and CEO of Comcast, said Zucker has "led the company with integrity and purpose.
"The success of NBC Universal puts us in a wonderful position as we plan our joint venture with GE," Roberts said. "We wish Jeff well in his future endeavors."
Zucker said he has a wide range of interests, including business, sports and journalism, and believes this has served him well in his career.
"I'm interested in politics," he said. "I have no plans to run for political office. Is it something I would consider? Yes."
Comcast has been tightlipped in its plans for NBC Universal when it takes over. One name that has surfaced as a potential new executive there is Robert Greenblatt, the successful programming chief at Showtime who stepped down when his contract ended this summer.