Ioane Teitiota and his wife moved to New Zealand from the low-lying Pacific island nation in 2007. He argued that rising sea levels make it too dangerous for him and his family to return to Kiribati.
Immigration authorities twice rejected his claims, so he appealed to the High Court.
In his decision, Judge John Priestley said Teitiota did not fit the definition of a refugee under international guidelines because he was not being directly persecuted.
The judge said if he broadened the definition, millions more people worldwide suffering from natural disasters or warfare would be eligible to become refugees.
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The judge said Teitiota and his children might have mounted a case to stay on humanitarian grounds had they not overstayed their visas.
"Unfortunately for the applicant, because he has chosen to remain illegally in New Zealand, he is, under current law, precluded from applying for an immigration permit on humanitarian grounds," he said.
Kiribati, an impoverished string of 33 coral atolls located about halfway between Hawaii and Australia, has about 103,000 people and has been identified by scientists as among the nations most vulnerable to climate change.
But the judge said that wasn't argument enough.
"The history of the last 3,000 years of human kind records huge movements of people, driven in some cases by overpopulation or scarce resources," he said. "But the globe is currently divided between independent sovereign states which would certainly resist unimpeded migration across state boundaries.