As part of the Unite to Remain pact in England and Wales, the Lib Dems will stand in 43 constituencies, the Greens will stand in 10 and Plaid Cymru will stand in seven.
It means the Greens will not field a candidate in York Outer, Harrogate and Knaresborough and Penistone and Stocksbridge.
Liberal Democrats leader Jo Swinson said: “I am delighted that this arrangement will help elect more pro-remain MPs in the next Parliament.
“In the 43 seats agreed today, as well as hundreds more across the country, it is clear that the Liberal Democrats are the strongest party of Remain.
“A vote for the Liberal Democrats is a vote to stop Brexit, so that we can invest the £50bn Remain bonuses in our public services and build a brighter future.”
Green MEP Molly Scott Cato told the Unite to Remain press conference that she hopes today will be seen as a "historic day", and she hopes the deal will "break the two-party stranglehold".
But the Electoral Reform Society criticised the move, saying polls show voters largely oppose parties having to stand aside for each other in deals like this.
Spokeswoman Jess Blair said: “Parties are feeling forced to game a voting system that fails to reflect the diversity of politics in 2019.
"It’s voters who lose out under this unfair First Past the Post system, where all votes not cast for the one winner go to waste. This forces people to hold their nose and vote ‘tactically’, while parties make deals between themselves on where to stand."
In York Outer, Liberal Democrat Keith Aspden will be contesting the seat against Conservative Julian Sturdy, who is defending a majority of 8,289.
The Lib Dems recently took control of City of York Council, in a coalition with the Greens, after the Conservatives lost all but two of their council seats.
The Liberal Democrats' candidate in Harrogate and Knaresborough, Judith Rogerson, will be looking to overturn a 18,168 majority to unseat sitting Tory Andrew Jones, a former Rail Minister.
And in the marginal seat of Penistone and Stocksbridge, Barnsley councillor Hannah Kitching is standing for the Liberal Democrats in the hope of taking the seat previously held by Angela Smith. Mrs Smith, a former Labour MP, joined the Lib Dems earlier this year but will be fighting another seat at the General Election. Green Party candidate Richard Trotman will step aside.
Elsewhere, In the Isle of Wight and Brighton Pavilion, the Greens will be given a free run, while in the constituencies of Richmond Park and Cheltenham, the Lib Dems will be unopposed by other Remain-backing parties.
Sian Berry, co-leader of the Green Party, said: "The crash-out Brexit the Tories are pushing for would be a disaster for people up and down England and Wales. And for action on climate chaos."