Kyara was the last orca to be born at a SeaWorld Park following the park's decision previous year to end its killer whale breeding program.
However marine mammal scientists have argued that keeping orcas in captivity is both physically and psychologically harmful to the animals, and have questioned SeaWorld's claims that orcas' life expectancy in captivity is comparable to the lifespans of orcas in the wild, the BBC reported in 2016.
As per the recreation center, the whale's ailment was not caused by being in imprisonment.
A post-mortem examination is to be conducted, meaning the cause of death will most likely not be confirmed for a few weeks.
The three-month-old whale was being treated at the park's Animal Hospital for an infection. Kyara and Takara are pictured here.
Kyara was the last orca born in captivity at the park after the company announced it would end its breeding program previous year.
"Additionally, the team was hand-feeding her in an effort to ensure she received the nutrition she needed".
Earlier this year another SeaWorld orca, Tilikum, died of a bacterial infection. None of the other whales at the park are exhibiting symptoms of illness, SeaWorld's statement said.
SeaWorld has announced plans to introduce new "natural orca encounters" in place of theatrical shows.
The film focused on Tilikum, an orca at SeaWorld Orlando who killed a trainer during a 2010 performance.
SeaWorld has 22 orcas left in the U.S. The youngest, Amaya, was born in December 2014.
"Forty orcas have now died on SeaWorld's watch", the animal rights group said in a statement.