The 28-foot juvenile whale beached in the shallows at Fort Pierce Inlet State Park Monday, TCPalm.com reported.
Construction equipment was used to pull the dead animal from the inlet onto a beach where officials examined it.
"Something must have been wrong for it to come to shore," Blair Mase, a federal marine mammal stranding coordinator, said. "It was thin and in poor body condition."
Scientists conducted the necropsy outside, a normal procedure given the mammal's size of 5,000 to 6,000 pounds, research biologist Megan Stolen said.
The whale was "emaciated" and should have weighed double that amount, Stolen, with Hubbs Sea World Research Institute, a non-profit arm of Sea World, said.
"It was definitely a very sick whale," she said. "Its stomach was virtually empty."
In Florida, humpback whales that die usually are juveniles, conservationists said.
"It is not common to have a fresh specimen," Mase said. "We should be able to learn a lot from it."