The Scottish Tory leader, 40, will not be leaving politics and intends to stay on as an MSP.
Her decision comes as the Queen approved suspend Parliament for five weeks, but a spokesman for the Scottish Conservatives said the decision was "not connected to today's Brexit developments in any way."
ITV News Scotland Correspondent Peter Smith on the impact of Ruth Davidson's resignation for the Conservatives in Scotland.
The former journalist, who has a 10-month-old son, is said to have been considering resigning for a while for “a mix of personal and political reasons".
Ms Davidson has been leader of the Scottish Tory party for eight years, during which she turned the Conservatives into the second largest party at Holyrood.
While her decision is said to be more personal than political, Ms Davidson and Mr Johnson do not see eye-to-eye on many issues.
Ms Davidson threw her support behind Mr Johnson's rival prime minister candidate Jeremy Hunt during the Tory leadership campaign having previously clashed with the Prime Minister when she campaigned for Remain in the 2016 European referendum, going up against pro-Leave Mr Johnson in a televised debate at Wembley.
Ms Davidson, who was at one point widely-tipped to become Conservative leader, took her first steps towards a life in politics when she joined the Tories in 2009, having previously worked as a journalist.
The 2011 Scottish Parliament elections saw her take a seat from the Glasgow region list.
Two months later, the then-party leader Annabel Goldie announced she would quit the post and Ms Davidson stood for the position.
The self-proclaimed “tough old bird” won the election and became party leader in November that year, gaining 2,278 first preference votes out of the 5,676 cast.
Since then, she has widely been credited with changing the party’s image to being more socially liberal, supporting LGBT rights and favouring extending same-sex marriage equality to Northern Ireland.
Ms Davidson was at the helm during the 2014 Scottish independence referendum, which finished with the No side winning by 55% to 45%.
The 2016 Holyrood elections saw the Scottish Conservative Party position itself as the main unionist party, in which it gained the second-highest number of seats in parliament.
She had switched to the Edinburgh Central constituency for that vote.
Ms Davidson and partner Jen Wilson welcomed a son, Finn, in October 2018, and the Scottish Conservative leader only returned from maternity leave to frontline politics in May.