The discovery of the whale's body near Gravesend follows the death of a young humpback this month.
A second whale was found dead in the Thames less than two weeks after a humpback nicknamed Hessy died near the same stretch of water.
The Port of London Authority confirmed that the suspected fin whale was discovered in the river at Denton, near Gravesend, on Friday morning.
Martin Garside, a spokesman for the PLA, said he was surprised to receive a call at 10 a.m. about a second dead whale as there were no live sightings.
“We are as puzzled as anyone by that. When I took the first call this morning, I thought the person was confused and they imagined the whale watching, ”he said.
The PLA sent a patrol boat to go look, with the same crew that found Hessy's body, who quickly confirmed that it was a dead whale. The crew managed to get a line around the whale and gently towed it to a PLA site, where the animal was lifted from the water and taken to the Zoological Society of London for post-mortem analysis, Garside said.
Rob Deaville of ZSL's cetacean stranding research program said: “Experts hope to access the whale for examination in the next few days, but there is no reason to assume that the two recent whale strandings in the Thames during last week they are on some linked path ”.
Hessy was first seen swimming in the Thames 11 days ago. The whale died a few days later.
A detailed postmortem examination found that Hessy was a 27-foot (8.37-meter) juvenile female who had not eaten recently and was "nutritionally compromised." While experts found a large parasite load within the hunchbacked intestine, there was no evidence of plastic ingestion.
Deaville said: “The main finding was a large wound on the lower part of the head, associated with a fracture along one of the jaws (lower jaw). Traces of blood clots around the fractured jaw and bleeding around the cut / torn surfaces indicate that the damage occurred before death and it was the team's opinion that the injuries were likely the result of a ship impact, and this is considered the main cause of death. "
Deaville couldn't rule out the possibility that the whale might have been hit before entering the Thames, and it already had its injuries when it was seen swimming in the river.
Garside described the deaths of the two whales as a "random coincidence." While it was rare for a whale to end up in the Thames, he said, a handful had been seen in the past decade.
In 2009, a juvenile male hunchback was found dead near the Queen Elizabeth II Bridge. Last year, a beluga whale was sighted off Gravesend, more than 1,000 miles (1,600 km) from its usual Arctic habitat.
Garside said the discovery of the dead whales was "sad and moving at the same time." He said he hoped that retrieving the whale's body and giving it to scientists would lead to an explanation for its death.