Johnson said he was "torn between family loyalty and the national interest."
Jo Johnson, the brother of UK Prime Minister Boris Johnson, has quit as an MP and higher education minister because of "unresolvable tension" between "family loyalty and the national interest".
His surprise resignation comes after his sibling expelled 21 MPs — including Winston Churchill's grandson — from his own party because they did not back his Brexit strategy.
It was not immediately clear whether his resignation was effective immediately or whether he would step down when new elections were called.
Johnson, 47, who was Conservative MP for Orpington, served as an MP under three PMs, David Cameron, Theresa May and finally his brother, Boris.
In 2018, Johnson quit the government over Brexit, calling for the public to have fresh say on quitting the European Union.
His position on Brexit puts him at odds with his brother Boris, who lead the Leave campaign in the 2016 referendum.
When he left the Theresa May-led government last year he said: "Hopes for the easiest deal in history have proved to be delusions."
His resignation is yet another blow for his older brother who suffered three major defeats in Parliament this week in his bid to derail a bill that would prevent the country from crashing out of the EU on October 31 without a deal.
A spokesman for the British leader's office nevertheless said in a statement that "the Prime Minister would like to thank Jo Johnson for his service."
"He has been a brilliant, talented minister and a fantastic MP. The PM, as both a politician and brother, understands this will not have been an easy matter for Jo," the statement also said.
Angela Rayner, the shadow education secretary from the main opposition Labour Party said that the resignation showed that "Boris Johnson poses such a threat that even his own brother doesn't trust him."
"We need a general election as soon as no-deal is off the table so that a Labour government can transform our education system and society so they work for the many, not just the privileged few," she added.
The Liberal Democrats, who welcomed within their ranks a defecting Conservative MP on Tuesday, asked on Twitter: "Jo Johnson can't stomach what his brother is doing in No 10 on Brexit, so why should you?"
Scotland's First minister Nicola Sturgeon from the Scottish National Party pondered the same during First Minister's Questions.
"(Former Scottish Conservative leader) Ruth Davidson can't stomach the direction Boris Johnson is taking the UK in. Boris Johnson's own brother can't stomach it. the question is, why should people of Scotland be expected to put up with it?"