Jack the cat escaped two months ago when his kennel flipped over at JFK Airport.
Last month, American Airlines announced Jack had been stowing away the whole time in the customs room.
Thousands of fans joined a Facebook page dedicated to finding the traveling cat.
American Airlines was planning to ship Jack back to California.
The Facebook page dedicated to Jack said the feline had extensive wounds that would not heal due to the malnutrition he suffered while he was lost.
Jack was euthanized on Sunday.
Customs officials said Jack was found in pool health on Oct. 25 after falling through the ceiling of the airport's customs area.
American Airlines offered condolences to Jack's owner, Karen Pascoe. Jack and her other cat, Barry, were traveling in separate carriers. Jack's carrier fell, allowing him to escape.
Jack's owners posted this status update on Facebook on Sunday:
"It is with tears that I must tell you that Jack has gone over the rainbow bridge. He was with Karen yesterday, and his condition was worsening. He was treated overnight, and she (and I) both had extensive conversations with the vets at Blue Pearl regarding his condition. Jack had extensive wounds on the back of his body, and the wounds were unable to heal because his skin had deteriorated due to the malnutrition that occurred while he was lost. Despite antibiotics, the infections were worsening, and his skin was continuing to deteriorate. He needed surgery to treat the wounds, but there was not enough available skin to close the wounds after the surgery. The vet compared his skin condition to having severe burns over 50-60 percent of his body. The vet was very clear that she had conferred with every possible doctor regarding options for Jack, but none of them left him with a substantial chance of survival and all of them involved him suffering. Jack had been through so much, and the last thing anyone wanted was for him to suffer more. Jack was bathed in love and crossed over just a few minutes ago.
"We thank everyone who has gone on this journey with us. We have been introduced to people we have come to not only respect, but love. We will continue our work on this page...and will also be starting a dedicated website in Jack's honor. We want people to understand the risks that attend putting an animal in cargo, and we hope to spur change in the industry so that no one else ever has to go through this again. We honor Jack, we honor all the other animals who have been killed, injured, or lost while being transported through cargo procedures, and we honor all of you who have taken the time to share your kindness and love with us.
"Thanks to all of you for your love & kindness. We still have 2 cats to transport...and a message to send to all the airlines and the government that is time to make sure all of our pets are safe when they travel. I'll be back on this page tomorrow...blessings to all!! RIP, Jack...we'll all see you soon."
RIP JACK: JACK THE CAT'S FACEBOOK PAGE