In a statement, Samaritans said the fund would put the money into projects that the family of the runner Claire Squires feel would have been important to her.
The charity said it was "deeply touched" by the support it had received since the death of Squires, who collapsed on Birdcage Walk, less than a mile from the finish line in Sunday's race.
Catherine Johnstone, chief executive of Samaritans, said: "Claire chose to run the marathon for Samaritans because her mother, Cilla Squires, has been a volunteer for the charity for 24 years.
"We desperately wish that it was not under these circumstances, but we have been overwhelmed by the response from people donating in Claire’s memory.
"These donations will be put into a tribute fund and, after discussions with the family, will go towards projects they feel would have been important to Claire."
Donations to Squires’ JustGiving page this morning stood at more than £330,000, with large numbers of contributions made after the news of her death was made public. Several donors expressed their condolences on the website. Samaritans had an income of £10.2m in 2010/11.
She had previously raised £1,430 for the Royal Air Forces Association by climbing Mount Kilimanjaro in Tanzania in March 2011.