Gentoo penguins (Pygoscelis papua) have a widespread breeding distribution across the sub-Antarctic and Antarctic. Population trends vary across their range, with increases recorded in the Antarctic and Atlantic sectors of the Southern Ocean, while other sub-Antarctic populations are decreasing. Macquarie Island is the only breeding site for gentoo penguins in the Pacific sector of the Southern Ocean and one of just two breeding sites within Australian territories. Eight island-wide censuses were undertaken between 1984 and 2017 to estimate the number of breeding pairs, with a follow-up chick census conducted in four years to calculate breeding success. The most recent census in 2017 recorded the fewest breeding pairs since counts began, with 2527 ± 66 gentoo pairs island wide. However, breeding success was the highest recorded at 0.99 chicks per nest. Trends in sub-populations around the island differed. However, island-wide breeding pairs have decreased by − 1.8 ± 0.4% per annum over the past 34 years, particularly driven by breeding colonies in the east-coast section of the island. This overall negative trend differs from the currently stable global trend, but mirrors what is happening in some other parts of the species’ sub-Antarctic range. We suggest based on a 50% decrease in breeding pairs over the species’ last three generations, and a lack of recent data from Heard Island, Australia’s other gentoo penguin breeding site, the species be considered for listing under the Australian Environment Protection and Biodiversity Conservation Act 1999.