The bill, which contains billions of dollars in additional domestic spending sought by House Democrats, passed 239-182 Thursday, with 15 Democrats and 167 Republicans voting against it, The Hill reported.
Because the House amended the Senate version of the bill, the measure must return to the upper chamber for consideration.
House members defeated several amendments offered by liberal Democrats that would have forced the Obama administration to withdraw troops from Afghanistan sooner than officials want, the Washington publication said.
As the House debated the bill, the Obama administration issued a statement strongly supporting the war funding but threatening a presidential veto of any bill that included "provisions that would undermine (the president's) ability as commander in chief to conduct military operations in Afghanistan."
The statement also threatened a veto of any bill "that includes cuts to education reforms." The supplemental appropriation includes $15 billion in education aid that would be offset partially by $800 million in cuts to new education programs, the House Appropriations Committee said.
"It seems only reasonable to defer some new activities and expansions in order to help address the urgent fiscal crisis facing our school systems," a committee statement read. "In addition, the rescissions in no way damage the future funding prospects in better economic times for these programs."
Republicans cried foul, calling the parliamentary maneuvers "political chicanery" designed to push through Democrats' domestic spending priorities. The Hill reported Republicans also complained that the votes were structured in such a way that made it impossible for the House to approve military spending without returning the legislation to the Senate.