Police were called around 4.30am today (August 23) to Hertsmere Road.
Officers arrived with the London Ambulance Service and a woman in her 20s was taken to hospital.
She is now being supported by specialist officers.
There have been no arrests but an investigation is underway.
Officers are appealing for anyone with information to get in touch.
A Met Police spokesperson said: “We are investigating an alleged rape which took place on Hertsmere Road, Canary Wharf.
“Officers were called at 04:25hrs on Saturday, 23 August and attended alongside the London Ambulance Service.
“A woman in her 20s was taken to hospital and is being supported by specially trained officers.
“At this time no arrests have been made, but officers continue to make urgent enquiries.
“Anyone with any information, or who was around the area at the time is urged to contact police by calling 101 or online, quoting CAD1371/23.
“Alternatively, you can contact the independent charity Crimestoppers anonymously on 0800 555 111.”
