The young male bird, which was dehydrated and starving, is thought to be only the fourth royal penguin to wash up there in more than a century.
He is believed to have come from a breeding colony in the sub-Antarctic Macquarie Island.
Vets said the bird, dubbed Happy Feet Jr, may have been drifting for a year.
Lisa Argilla, a vet at Wellington Zoo, said the penguin had possibly struggled to find enough food or had had problems hunting and had come ashore as he needed to go through his seasonal moulting.
He was found on Tora beach, on the coast to the south of Wellington.