The bill, which also will freeze pay for congressmen, was approved 261-154, The Hill reported.
People serving in the U.S. military are exempted.
Some 43 Democrats voted for the bill while 10 Republicans voted against it.
Darrell Issa, R-Calif., chairman of the House Oversight and Government Reforms Committee, said the bill would help control the costs of the federal government.
Obama's executive order had given federal workers a 0.5 percent pay raise that would go into effect at the end of March.
The White House had opposed the bill, saying raises were needed to enable the government to compete in "attracting and retaining the nation's best and brightest individuals for public service."
Democrats charged Republicans put the costs of deficit reduction on the backs of federal workers.
Rep. Elijah Cummings, D-Md., said federal employees had contributed "more than $100 billion" toward reducing the federal deficit.
Issa countered the $100 billion was spread out over 10 years.
Two Republicans who voted against the freeze, Reps. Frank Wolf of Virginia and Frank LoBiondo of New Jersey, said federal law enforcement officers and first responders should not have their pay cut because their work requires them to put their lives on the line.
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