Cook’s Petrel (Pterodroma cookii), a trans-equatorial migrant endemic to the New Zealand archipelago, is today endangered and restricted to island habitats at the northern and southern extents of its former range. To improve the limited knowledge of the breeding habitat of this species, we combined an island-wide survey, the mapping capabilities of geographic information systems, and logistic and autologistic analyses to examine burrow distribution and habitat use of the world’s largest population of Cook’s Petrel, on Little Barrier Island (Hauturu). Our results show that, on this island, Cook’s Petrel breeds predominantly above 300 m above sea level, on steeper slopes, closer to ridge tops, and in unmodified forest habitats with low and open canopies and greater numbers of large stems compared to the available terrain and habitat. Within these habitats above 300 m, densities of burrows are 0.04 burrows m^–2. Through comparisons with habitat data from two low-altitude colonies, we conclude that the current distribution of this population is a result of habitat selection and historical human-mediated impacts. We suggest that mature forest habitats, close proximity to ridge tops, and steep slopes are key habitat requirements for this species. A large amount of suitable habitat is available for Cook’s Petrel on Little Barrier Island and the recent removal of introduced predators is expected to result in an expansion of this population. The results of the current study provide useful information to aid in the restoration of former colony sites on other islands and the New Zealand mainland.