The decision is a major rebuke to the House leadership under Speaker John Boehner, and McCarthy, the current majority leader looking to win the speaker's job.
Rep. Raul Labrador, R-Idaho, said it took several votes to determine the winner of the endorsement. Rep. Jason Chaffetz,
R-Utah, had "some support," McCarthy had "no support" and Webster had the most support, he said.
Thursday, the Republican conference will vote on who to nominate as their speaker candidate. But that vote only requires a majority -- and the crucial hurdle for McCarthy will be whether he can get 218 votes on the floor when the full House votes October 29.
"It's a healthy debate we'll have a vote on the floor and in conference tomorrow," McCarthy said Wednesday. "Just like going through any other primary - (it) will be the power of ideas."
Pressed about not getting to 218 on Thursday, McCarthy replied, "You don't need to get to 218 until you get to the floor."
But if the Freedom Caucus maintains its unity through the floor vote, it could force McCarthy -- or the eventual winner - through multiple ballots for the first time in nearly a century.
In a statement, the group emphasized its members desire for change.
"It is clear that our constituents will simply not accept a continuation of the status quo, and that the viability of the Republican Party depends on whether we start listening to our voters and fighting to keep our promises," the group said. "We accordingly believe that, under the present circumstances and without significant changes to Conference leadership and process, Rep. Daniel Webster would be best equipped to earn back the trust of the American people as Speaker of the House."
Rep. Matt Salmon promised "over 30 votes" would go to Webster.
"Our intention is to go all the way to floor unless real changes are made to how the House is run," Labrador said. "Right now our intention is to stick together all the way to the floor."
Decision not unanimous
Webster has been considered a long-shot candidate for the position. In January's Speaker election, he only got 12 votes in his bid to unseat Boehner.
Chaffetz, the chairman of the House Oversight and Government Reform Committee (whose hearing room the caucus met in to make its choice), announced his own longshot bid for speaker over the weekend, though he as called himself an "underdog" in the race and spoken of McCarthy's popularity.
"I went out, put my best foot forward," Chaffetz said. "They decided what they decided. I'd like to get every vote I could. Some were frustrated that I would endorse the nominee but that's our process and that's what I believe.
"My candidacy has always been based on the idea that somebody needs to bridge the divide and based on tomorrow's vote I will endorse the nominee but we have to address the divide that's in the conference," he added.
The group was not unanimous in its vote, Labrador said, but did meet the more-than 80% threshold. The caucus' rules state that if 80% of the members agree on a position, the entire group will stand behind it. "He wasn't my first choice but I promised all along I'd go along with the group," Salmon said of Webster.
The caucus met for nearly two hours before reaching its decision.
Already, however, there appears to be some division coming out of the meeting. Not all Freedom Caucus members appear to be on the same page for taking this fight to the floor.
"I don't think we've committed to anything on the floor yet," Rep. David Brat, R-Virginia, told reporters.