During a press conference Tuesday, Boehner was asked if he agreed with House Intelligence Committee Chairman Mike Rogers on Syria.
“I think their effort to help the right set of rebels in Syria is in our nation’s best interest,” Boehner said.
On Monday, the House and Senate Intelligence committees approved President Obama’s plan for the CIA to begin a covert operation to arm the Syrian rebels.
Although he signed off on the plan, Chairman Rogers said he remains concerned that weapons could end up in the hands of Islamist militants.
"It is important to note that there are still strong reservations," Rogers said. "We got a consensus that we could move forward with what the administration's plans and intentions are in Syria, consistent with committee reservations."
One of the strongest groups fighting against Syrian President Bashar Assad is Jabhat al Nusra, an Islamist group that pledged its loyalty to al Qaeda last month.
According to the Guardian, the Free Syrian Army, the main armed opposition group, is losing fighters and capabilities to Jabhat al-Nusra, strengthening the terrorist group.
The Obama administration has said it wants to support only those insurgent groups that are not terrorist organizations.
Most Americans oppose sending arms to Syria. A Pew Research Center poll conducted last month that found 70 percent are against the U.S. and its allies sending arms and military supplies to anti-government groups fighting in the civil war.