He will also step down as an MP for Orpington at the next election.
Jo worked as the transport minister in Theresa May's government, but quit in November 2018, citing her handling of Brexit as the reason for his resignation.
In the past he has called for a second referendum, and despite he and his brother's differences over Brexit, he got behind him during his Tory leadership campaign.
It's been an honour to represent Orpington for 9 years & to serve as a minister under three PMs. In recent weeks I've been torn between family loyalty and the national interest - it's an unresolvable tension & time for others to take on my roles as MP & Minister. #overandout
- Jo Johnson (@JoJohnsonUK) September 5, 2019
Following his election, Boris brought his brother back into government, offering him a ministerial position.
Today's shock departure comes a day after the Prime Minister lost his motion to hold a snap general election.
Jo's brother failed to get the two-thirds majority he needed - under the rules of the Fixed Term Parliament Act - to force a snap poll through the House of Commons.
The motion was passed by 298 votes to 56, but as Labour abstained from voting, it failed to meet the threshold and an election will not be held.
The next scheduled election is not until 2022.
Following the result, Johnson said Jeremy Corbyn 'has become the first leader of the opposition in the democratic history of our country to refuse the invitation of an election'.
He went on: "I can only speculate as to the reason behind his hesitation. The obvious conclusion is he does not think he can win."
Johnson called for a general election after MPs voted 327 to 299 in favour of the Brexit delay bill, in a bid to block a No Deal Brexit on 31 October.
Announcing his wish for an election, Johnson said: "There is only one way forward for the country. The House has voted repeatedly to leave the EU, but it has also voted to delay actually leaving.
"Today, I'm afraid it has voted to scupper any serious negotiations."
Earlier this week, 21 'rebel' Tory MPs who defied the whip and voted against the Government were kicked out of the party and will not be allowed to stand as Conservatives at the next election.