The Royal Penguin being cared for by Wellington Zoo died overnight.
Zoo staff say the cause of death is believed to be multiple organ failure.
The penguin was found dehydrated and critically ill at Tora on the Wairarapa coast on Sunday and has been at the zoo since Monday.
Vets had given the penguin only a 20-30% chance of survival and said although they are disappointed "this is often the sad reality of caring for wild animals".
The juvenile, dubbed Happy Feet Junior, was discovered in a critically ill condition in Tora Bay, 2000 kilometres away from its home in the Sub Antarctic.
The penguin had suffered from severe dehydration which had led to since caused kidney failure.
"Something's happened out at sea, he's not found enough food. Something's gone wrong with his hunting and he's come ashore because he has to malt, physiologically these birds need to malt once a year," Wellington Zoo Vet Lisa Argilla said.
Royal Penguins rarely venture to the North Island as the climate is too warm.
However this is not the first time Wellington Zoo vets have been called on to nurse a lost penguin.
An Emperor Penguin nicknamed Happy Feet spent two months in a specially designed ice box at Wellington Zoo after he was found washed up on a Kapiti Coast Beach in 2011.
Happy Feet rose to national fame before he was released near Campbell Island.