Opposition to Boehner doubled from the last election for Speaker in 2013, when a dozen Republicans voted against him. He ultimately received 216 votes, enough to fend off an embarrassing vote on a second ballot but plenty to reinforce the notion that Boehner is struggling to maintain control over restive House Republicans.
The dramatic scene played out before live television cameras, as members were called upon one-by-one to stand and name who they were backing to serve as the next Speaker.
Despite the opposition facing him, Boehner was greeted by a standing ovation after he was nominated by Rep. Cathy McMorris Rodgers on Tuesday and his wife, Debbie, watched the floor action from the Speaker's box.
Shortly after winning his spot Tuesday afternoon, an emotional Boehner called improving the economy and creating more opportunities for the middle class "our vital task."
"We'll begin on common ground," Boehner said, adding later "All I ask is that we disagree without being disagreeable."
He joked that his door is always open, but "don't get carried away with it."
Behind the scenes, Republicans who opposed Boehner are beginning to face the fallout. Florida Reps. Richard Nugent, who voted against Boehner, and Daniel Webster, who challenged him, were removed from the House Rules Committee on Tuesday, according to multiple sources.
Rules Committee Chairman Pete Sessions suggested the decision to remove the two GOP members came from Boehner, telling reporters he had only spoken with Webster.
"The committee works at the behest of the speaker and the speaker -- I believe any speaker -- would want and need a person focused on that agenda," Sessions said.
Sessions said he was surprised these members broke with Boehner, adding "sometimes there are casualties and there are changes, and people make decisions to do things knowing sometimes there can be consequences."
But the Texas Republican appeared irked at the pressure from the grassroots activists these Boehner opponents drummed up before the vote.
"The onslaught that has happened over the last two or three days has taken a number of members by storm. Their district offices, their Capitol Hill offices have been inundated by people who seemingly drew conclusions that we didn't even have time to go home and defend," Sessions said.
A senior House GOP leadership aide indicated other members could also face some type of repercussions for their public rebuke of Boehner.
Rep. Tim Huelskamp of Kansas said he and other Republicans who voted against Boehner fear some type of retribution. He said he was told by a committee chair recently that he was in line for a subcommittee chair post but then after he publicly announced his new post it was revoked, and he suggested his criticism of the leadership cost him the job.
Florida Rep. Ted Yoho, who was nominated by a GOP colleague to replace Boehner and voted for himself, struck a more conciliatory note. He told reporters Boehner is "the speaker of the House and I look forward to following his lead."
Boehner begins the 114th Congress with a new Republican controlled Senate and big plans to enact a conservative agenda. President Barack Obama will meet with congressional leadership next week.
But the contentious election just to secure Boehner's job is a sign that the same dynamic he's seen in the last four years -- resistance from conservatives -- will continue to hamper his ability to govern the House.
After the vote, one of the Republicans who voted against Boehner, Huelskamp said the vote re-electing Boehner "sends a clear message that that U.S. House Republican majority is status quo -- more of the same."
He said the 25 members who voted for someone else or declined to vote was less about Boehner personally, but about his leadership's record of bringing major legislation to the House without enough input from members.
Sessions, a Boehner ally who will help set floor debate parameters, said "that's not the plan" and insisted there would be open deliberations with members about what bills go to the floor.
Oklahoma Republican Rep. Tom Cole, a defender of Boehner's, said that because of the larger GOP majority in the House, the speaker can afford to lose some members. And he suggested those who broke with Boehner are likely to continue resisting his legislative strategy going forward.
But he warned those who regularly rebel may end up hurting their own cause.
"There's always a little bit of fragmentation that occurs because again, people know they can go their own way and you can still get the legislation passed. And I think you saw a certain amount of that today. 'Well the speaker's going to win anyway, and this will help me at home with my right wing. The problem is, if that's your reasoning, you're going to be subjected to that every single time, and you're going to start to lose influence," Cole said.
The speaker began reaching out to members the day after the midterm elections, and he and his allies continued to make calls and appeals for support right up until the vote on Tuesday afternoon, according to a senior House GOP leadership aide. As the top fundraiser for his party he raised over $100 million for GOP members and candidates and traveled to more than 150 events over the 2014 midterm cycle.
One of the GOP members who broke with Boehner, North Carolina Rep Walter Jones, argued the current political system helps keep leaders like Boehner in place because they help colleagues with campaign donations.
"This place, it's all about money. Both parties, everything is about raising money for the next election. That's what complicates good policy -- is the next election and raising money," Jones said.
Sessions said the new Republican majority on Capitol Hill has to have a better PR effort to ensure the public gives it credit -- both with its own members and the public -- for what it is doing to cut spending.
"We've got to do a very good job and sell what we do and if we sell what we do, then people will see it and i believe come to our side, including our friends in the tea party who very very much want to see our party win the presidency," Sessions said.
Freshman Republican Rep Lee Zeldin, who backed Boehner, told CNN it was time for the House GOP members to move on and start focusing on coordinating with the new Republican controlled Senate.
"It's important this this entire Republican conference regardless of whether you are leadership or rank and file, whether you are conservative or moderate, or whether you are from New York or from Oklahoma that we work together to move American forward."
The No. 2 House Democrat, Rep. Steny Hoyer of Maryland, told CNN he didn't think there would be any real fallout for Boehner of the high-profile spat on the House floor.
"He won," Hoyer said. "In two weeks no one will remember what the vote was. He's the speaker."