The Pakistani-origin first Muslim woman to serve in the cabinet posted a message on Twitter announcing she "can no longer support Govt policy on #Gaza".
"With deep regret I have this morning written to the prime minister and tendered my resignation. I can no longer support government policy on Gaza," the Daily Mail cited her as tweeting.
British Prime Minister David Cameron, however, has refused to say whether Israel's actions in Gaza were "criminal".
Warsi was the senior minister of state at the foreign office and faith minister at the department for communities and local government.
There were no further details given about her decision to resign, or the timing.
On Monday night she attended a ceremony in Westminster Abbey here to mark the centenary of the outbreak of World War I, the report said.
She resigned as displaced Gazans began returning to their homes from UN shelters after the latest ceasefire between Israel and Hamas took effect Tuesday.
The 72-hour truce, which started at 8 a.m. Tuesday was agreed to by both sides in the month-long conflict.
Cameron has faced criticism, including from Labour Party leader Ed Miliband, for failing to take a tough enough line with Israel over the crisis.
On Monday, the the prime minister refused to say whether he believed Israel's actions in Gaza were "criminal".
He said the UN was "right" to condemn an airstrike near a school in Rafah that left 10 people dead.
But he stopped short of endorsing secretary general Ban Ki-Moon's description of the attack as a "moral outrage and a criminal act".