The learning disability charity was the official charity partner of this year's event which was pushed back from its usual date in April until 4 October as a result of the pandemic.
But last night, the marathon organisers announced the ongoing concerns about Covid-19 meant the event’s traditional mass-participation element would now not go ahead.
The partnership had given the charity 250 guaranteed places in the race.
Edel Harris, chief executive at Mencap, said: "We're obviously disappointed the usual event isn't going ahead - but know that the London Marathon events team have been working hard to find alternatives in this really difficult year.
“We had lots of ambitious and innovative ideas for race day about how to use the partnership to put learning disability on the map, and raise £1.5m for people with a learning disability.”
Harris described the pandemic as a “tough time for fundraising” and encouraged supporters to donate to the charity’s runners, despite the setback.
“We're especially thankful to our incredible Team Mencap runners, including our brilliant runners with a learning disability, and hope they will continue to run for us in the coming years.”
“We are determined to still make the most of our charity of the year partnership by raising as much money as possible to make positive change and tackle stigma around learning disability."
In an announcement made on the Virgin Money London Marathon website yesterday, organisers said that elite athletes would be able to compete in the marathon on an enclosed course in St James’s Park.
“Elite races for men, women and athletes will take place on an enclosed looped course in St James’s Park in a secure biosphere (a contained safe environment like that of Formula 1 and England cricket) and times will be eligible for Olympic qualification,” the statement read.
Runners who had booked a place in the 2020 event will be able to take part in the race by running the 26.2 mile marathon distance from home, or another location, organisers said.
All runners and charities will be able to defer their place to a future London Marathon, either in 2021, 2022, or 2023, and the 2021 marathon will be moved from its traditional April date to 3 October, to give the best chance for the mass race to return.
Last year, the mass-participation event raised a record £66.4m for charity.