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Boehner defeated House Democratic leader Nancy Pelosi 220-192 in a vote on the opening day of the 113th Congress and vowed to use his second term to shrink the national debt of $US16 trillion to prevent it from "draining free enterprise."
The Ohio congressman narrowly avoided the embarrassment of having to go to a second round of voting, as 12 conservatives held back their support for him. It was the closest margin of any speaker vote since 1997.
But without a challenger from inside his party, Boehner's re-election was never in doubt even though he has struggled to control an unruly group of fiscal conservatives in his caucus.
True to form, the often emotional Boehner shed a tear or two as he took the gavel and spelled out the challenges ahead.
"Our government has built up too much debt. Our economy is not producing enough jobs. These are not separate problems," Boehner said.
"At $US16 trillion and rising, our national debt is draining free enterprise and weakening the ship of state."
Questions were asked about Boehner's speakership when conservative Tea Party-backed lawmakers delivered him a stinging defeat in December by rejecting a proposal of his during talks with President Barack Obama to raise taxes on millionaires.
Boehner also came under fire for voting on Tuesday for a compromise deal to prevent the U.S. economy from falling off the so-called fiscal cliff and for being slow to approve aid for victims of Superstorm Sandy in the Northeast.
A tough job
"Being speaker today is no bargain, I tell you," Republican Representative Peter King of New York told MSNBC's "Morning Joe."
Widely seen as having lost the "fiscal cliff" fight with Obama by accepting tax increases, congressional Republicans are keen for a rematch and they will get the chance soon.
Debate is likely to be fierce when lawmakers deal with planned spending cuts for military and domestic programs that are due to start in February. Around that time, Congress is likely to take up the thorny issue of extending the "debt ceiling" - the limit of how much the federal government can borrow.
Boehner was the Republicans' front man in fiscal talks with Obama but stepped aside for Senate Minority Leader Mitch McConnell who struck a dramatic New Year's Eve deal with Vice President Joe Biden.
The stress of recent weeks seems to have got to Boehner, who cursed at Senate Majority Leader Harry Reid at the White House twice after a meeting last week, according to Senate aides.
Reid had accused the Republican of running a "dictatorship" in the House and being more interested in keeping his speakership than in cutting a fiscal deal.
The son of a bar owner, Boehner had a tough upbringing. He shared one bathroom with his 11 siblings and worked in the family business while still a child.
He was elected speaker after the 2010 midterm elections when a Tea Party surge helped Republicans take the House from the Democrats.
Pelosi, his predecessor and now Democratic minority leader, presented the gavel again to Boehner on Thursday just after he won re-election.
"I know all too well that we will not always agree," Pelosi said. "But I hope, with all my heart that we find common ground that is a higher, better place for our country."
Fellow Republicans, not Democrats, have been landing some of the toughest blows on Boehner, notably New Jersey Governor Chris Christie who launched a tirade against the speaker for postponing an anticipated vote on a $60 billion storm aid package for the victims of Sandy.
King, who was among Boehner's critics, was more forgiving on Thursday after the speaker agreed to abruptly reverse course and set a timetable to approve the storm relief.
"John is really a voice of reason in our conference, despite some of the things I said yesterday," King told NBC's "Today."
Seeking to explain the difficulties of Boehner's job, Representative Hal Rogers, a Kentucky Republican, borrowed a line from fellow southerner Bill Frist, who once described leading Republicans in the Senate as: "It's a lot like being a caretaker of a cemetery - a lot of people under you but nobody listens."