Boehner told Obama he was "disappointed" by his stance, The Hill reported Friday.
"Given the long history of using debt limit increases to achieve bipartisan deficit reduction and economic reforms, the Speaker was disappointed but told the president that the two chambers of Congress will chart the path ahead," an aide said. "It was a brief call."
The increase will likely be needed next month for the government to continue operating.
Republicans have tied an increase in the debt ceiling to repeal of the Affordable Care Act, commonly known as Obamacare, but the president has said he will not be "extorted" to get Congress to raise the debt limit.
Speaking to automotive workers Friday in Kansas City, Mo., Obama charged Republican tactics on the debt ceiling were "the height of irresponsibility."
Boehner this week urged the president to work with Senate Majority Leader Harry Reid, D-Nev., to negotiate a deficit reduction package.