The Ohio lawmaker won a second term on the post with 220 votes. Boehner lost only a handful of votes in the GOP-controlled house. Democratic leader Nancy Pelosi got 192 votes.
The 113th Congress convened early Thursday and faces the same issues that plagued the 112th Congress -- one of the least productive in more than 60 years.
There are now 81 women and a record number of female senators in the House. The first openly Hindu member, the first Buddhist senator, and the first openly gay senator all took the oath Thursday.
Addressing the 80-plus new members, Boehner told them that if they came "to see your name in lights or to pass off political victory as accomplishment, you have come to the wrong place. The door is behind you."
"If you have come here humbled by the opportunity to serve; if you have come here to be the determined voice of the people; if you have come here to carry the standard of leadership demanded not just by our constituents but by the times, then you have come to the right place," he said.
Boehner has had a rough few weeks. He turned to Senate Republican Minority Leader Mitch McConnell to negotiate a deal with the white house to avoid the so-called "fiscal cliff."
Also, Boehner was booed when members learned he would not allow a vote on the $60 billion aid package for Superstorm Sandy.
The House will vote Friday on $9 billion in aid for the areas hit by the storm, and vote on the remaining $51 billion by Jan. 15.
The new Congress will have to deal with automatic spending cuts to defense and domestic programs that were put off for eight weeks and also tackle the question of raising the debt ceiling.
The Associated Press contributed to this report.