The man, who has not been named, reportedly collapsed after he crossed the finishing line.
He immediately received medical attention but was pronounced dead when he arrived at hospital.
The event's organisers, Virgin Money, expressed their "sincere condolences" to his family and pleaded for their privacy.
"We will not be releasing any further details of this tragic incident and would ask for your understanding in this matter," a statement read.
"We would like to emphasise that our immediate concern is for the family of the deceased.
"Our thoughts and deepest sympathies are with them at this difficult time."
In all, 36,000 competitors took part in the high-profile 26.2 mile event, with the men’s elite race won by Kenyan Wilson Kipsang.
The race, which started at Blackheath and Greenwich parks and ended on The Mall, received huge support as fans gathered in the sunshine to cheer on the runners.
Compatriot Edna Kiplagat finished first in the women's event, while Britain’s Mo Farah had to settle for an English record in eighth place in the men’s race.
- Sports & Recreation
- Virgin Money