The standoff between President Donald Trump's administration and the global entertainment conglomerate is the first crisis facing Walt Disney's new CEO Josh D'Amaro.
Unlike the last battle with Kimmel that centred on free speech, this time the FCC is targeting Disney's track record of diversity and inclusion practices, according to the order. The review names eight ABC stations owned by Disney.
Disney has until May 28 to respond.
The FCC has not revoked a broadcast licence in more than four decades and any effort by the agency to do so would typically be a lengthy process that requires a hearing in front of a career administrative law judge.
On Thursday, Kimmel did a send-up of the annual White House Correspondents' Association dinner on his ABC show, joking that First Lady Melania Trump had "a glow like an expectant widow."
The joke was made three days before the actual black-tie dinner, celebrating press freedom and free speech, in Washington. The president and the first lady were rushed from the dinner following an assassination attempt.
Disney said it had received the FCC order, adding it has "a long record of operating in full compliance with FCC rules and serving their local communities with trusted news, emergency information, and public-interest programming."
The company said it is "prepared to show that through the appropriate legal channels."
The stations are located in Fresno, Los Angeles, Chicago, San Francisco, New York, Philadelphia, Houston and Durham, North Carolina.
On Monday, the Trumps called for ABC to fire Kimmel, the latest incident of the White House pushing back on free speech that has roiled the world of late-night comedy and the press.
During his monologue on Monday night's show, Kimmel said the "expectant widow" comment "obviously was a joke about their age difference" that had been misconstrued. Trump will be 80 in June, and his wife turned 56 this month.
"It was not by any stretch of the definition a call for assassination," Kimmel said.
A Disney spokesman could not be reached for comment about Kimmel, who survived a previous call for ABC to fire him.
