Johnson, also a Conservative, removed the 21 MPs from the party, which means they will not be allowed to run for election.
“I cannot stand by as good, loyal moderate Conservatives are expelled,” Rudd said in a post on Twitter announcing her resignation. She also posted her two-page resignation letter.
Having Rudd sign on to Johnson’s Cabinet was considered a coup for the new Prime Minister, and she was considered the most important Remainer in his government.
Rudd’s resignation follows that of prime minister’s brother, Jo Johnson, resigned from Parliament, saying he was “torn between family loyalty and the national interest.”
Rudd addressed the prime minister in the letter, saying she joined the Cabinet in “good faith” and leaving was a difficult decision.
She said had accepted in joining Johnson’s government that ” ‘No Deal’ (Brexit) had to be on the table, because it was the means by which we would have the best chance of achieving a new deal to leave the EU on 31 October.
“However I no longer believe leaving with a deal is the government’s main objective,” she wrote.
Johnson, who has been prime minister for six weeks, expelled 21 Conservatives, including Winston Churchill’s grandson Nicholas Soames and Ken Clarke, the longest serving member of Parliament, after they voted to block the prime minister’s plan to leave the EU without a deal.
“This short-sighted culling of my colleagues has stripped the Party of broad-minded and dedicated Conservative MPs. I cannot support this act of political vandalism,” she wrote. “Therefore, it is with regret that I am also surrendering the Conservative whip.”
After losing the vote, Johnson said he would call for snap elections on October 15 rather than be forced to request another “pointless delay” to the Brexit process.
Johnson lost his first bid to hold an election on Wednesday, but decided to schedule another vote on the issue in the House of Commons on Monday. Opposition parties came out with an unusually united front on Friday, saying they would not support it.
The bill that would order Johnson to seek an extension to the Brexit deadline was approved by the House of Commons on Wednesday and House of Lords on Friday.
The bill becomes law if Queen Elizabeth approves it on Monday.
Rudd had been home secretary from July 2016 to April 2018
. She previously served in the government as secretary of state for energy and climate change, parliamentary under secretary of state for climate change and assistant government whip.