Kilar has long been rumored to be exiting the company as it faces stiff competition from Netflix Inc, Amazon.com Inc as well as Google Inc and Apple Inc.
Hulu chief technology officer Rich Tom is also leaving, according to the post.
Kilar gave no reason for his departure or indicate his future plans. Hulu did not name a replacement for the executives.
Kilar, Hulu CEO since July 2007, last year steered the company to $700 million in revenue and grew subscribers to 3 million. More than 200,000 new subscribers have signed up with the service in the last seven days, he noted.
"My decision to depart has been one of the toughest I've ever made," Kilar wrote. "The things that have clearly brought the most joy to my heart (and what I believe to be the most important inputs in our business) have been this team and the values and principles we hold dear."
Still, the popular service, which started primarily as a free site for people to catch up on television shows they might have missed, has had a rocky path over the last five years.
Part of the problem stems from its complicated ownership structure involving media conglomerates Walt Disney Co, News Corp and Comcast NBC Universal, and how much content each should make available to Hulu.
The owners face a dilemma: The success of Hulu could potentially eat away at the lucrative business of getting cable companies to pay for programming. Furthermore, it is now building out its own stable of original content exclusive to Hulu.
Disney CEO Bob Iger said in a statement that Kilar had been "an integral part of the Hulu story, transforming it from an interesting idea into an innovative business model that continues to evolve... We appreciate what he's built, and we share his confidence in his team's ability to drive Hulu forward from here."
A statement from News Corp CEO Rupert Murdoch said Kilar had helped build Hulu into one of the leading online video services and called the company "incredibly well positioned for the road ahead."
BTIG analyst Richard Greenfield expects News Corp's Fox to buy out its partners in the venture this year.
"With full ownership of Hulu, FOX accelerates Hulu's push into original programming and explores adding cable network content to create a virtual MVPD (multichannel video programmer distributor) service," Greenfield said in a January 3 research note.
Comcast, the third partner in the venture declined to comment on Kilar's departure. Unlike Disney and News Corp, Comcast does not have any management control of Hulu, which was a regulatory condition related to its acquisition of NBC Universal in 2011.
Hulu put itself on the block in 2011 with suitors including Google, Amazon, DirecTV Group and Dish Network Corp, Reuters reported at the time. Talks collapsed over the price of the deal.
Private equity firm Providence Equity Partners said in October last year that it had sold its 10 percent stake in Hulu to the remaining owners.
Kilar's name surfaced as a potential candidate for the top job at Yahoo Inc after Scott Thompson resigned last year but Kilar removed himself from consideration.
(Reporting By Jennifer Saba and Liana Baker in New York; Editing by Gunna Dickson and Tim Dobbyn)
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