Hoiho surged into first place in the second week of the competition, finishing with 6328 votes, after initially trailing the karure Chatham Island black robin, organisers said. The karure came in second and the kākāpō third.
The results of the competition, which attracted more than 52,000 verified votes, were announced on Morning Report on Monday.
The yellow-eyed penguin is unique to Aotearoa New Zealand and is thought to be the world's rarest penguin species, according to Forest & Bird which runs the competition. The are found along the east coast of the South Island, on Rakiura Stewart Island, and the Auckland and Campbell Islands.
The hoiho attracted high-profile endorsements, including from conservationist Dr Jane Goodall, former prime minister Helen Clark and Labour leader Chris Hipkins.
Its campaign was backed by Dunedin locals, and supporters included the Highlanders rugby team, and Emerson's Brewery, which crafted a special pale ale in honour of the "people's penguin".
"This spotlight couldn't have come at a better time," Forest and Bird chief executive Nicola Toki said. They were vulnerable to predators and dog attacks, and are at risk of being caught in set nets at sea.
The Yellow-Eyed Penguin Trust reported the number of mainland breeding birds had dropped by 78 percent over the last 15 years.
"This iconic penguin is disappearing from mainland Aotearoa before our eyes," Toki said.
The nationally endangered bird, whose te reo Māori name hoiho means 'noise shouter', is notoriously shy despite its loud, shrill call.
Ellen Rykers from Forest and Bird earlier said it was a chance to celebrate Aotearoa's "amazing" native birds.
"It's also an opportunity to highlight that more than 80 percent of them are in trouble, or serious trouble, and they really need our help."
Rykers said this year's competition had more of a homegrown feel, after a campaign by US talk show host John Oliver in 2023 led to a landslide victory for the pūteketeke (Australasian crested grebe).
"We have seen some amazing support from some New Zealand celebrities this year. So Sam Neill just endorsed the pukunui - the southern NZ dotterel - and .. Paddy Gower's just supported the Adélie penguin."
Voters were able to cast their ballots for up to five birds on the online poll, from a selection of 74 "candidates".
The top 10 votes:
- Hoiho yellow-eyed penguin (6328)
- Karure Chatham Island black robin (5442)
- Kākāpō (4548)
- Ruru morepork (4467)
- Kea (4206)
- Pīwakawaka fantail (4205)
- Takahē (3892)
- Tawaki piki toka eastern rockhopper penguin (3834)
- Kōkako (3445)
- Toroa Antipodean albatross (3415)
