The victim was pronounced dead at the Bow Roundabout at about 16:45 GMT on Friday, the Metropolitan Police said.
The crash also involved a lorry and the driver of this vehicle has been arrested on suspicion of causing death by dangerous driving.
Last month a 58-year-old man was killed in a collision with a tipper truck.
Transport for London (TfL) said at the time that he was the first person to be killed on the superhighway network.
Four priority lanes for cyclists have been painted blue around London, and another eight are due to open within the next four years.
The safety of the Bow Roundabout was questioned on Wednesday by John Biggs, a Labour member of the London Assembly.
He called on Mayor Boris Johnson to "get an urgent grip on this situation and show leadership to make our roads safe for cyclists".
"TfL have previously said that there is nothing that they can do to make the roundabout safer, without causing traffic jams.
"It is time they bite the bullet and accept longer journey times for motorists in exchange for keeping pedestrians and cyclists safe."
TfL has yet to comment on Friday's crash.
The A11 has been partially closed while investigations take place.
A 34-year-old woman has become the second person in three weeks to die at a busy junction on a cycle superhighway in east London.