Sea urchins are keystone herbivores in many marine benthic habitats and can significantly influence coral-algae phase shifts and reef carbonate budgets. Hall Bank Reef in Western Australia is a unique high latitude reef with high hermatypic coral cover but lacking macroalgae and soft corals. Since the reef status is thought to result from grazing of the urchin Centrostephanus tenuispinus, this study was focused on evaluating bio-erosion by C. tenuispinus with respect to size structure and seasonality. Monthly samples of urchins were collected during 2014–2016 and gut composition was analysed. Gut evacuation rates were calculated using urchins dissected at time intervals up to 96 h. Reworked CaCO3 was calculated using caged urchins in a nearby seagrass bed. Mean percentages of organic, CaCO3, and siliceous components in C. tenuispinus gut contents were 86.3 ± 3.2, 10.3 ± 2.8, and 3.4 ± 1.5%, respectively. Gut evacuation rates for autumn, winter, spring, and summer were 0.70, 0.24, 0.48, and 0.72 day −1. Bio-erosion rates were significantly higher in summer (3.5 g CaCO3 m−2 day−1) than in winter (1.3 g CaCO3 m−2 day−1) and higher rates recorded for large urchins. Urchin bio-erosion was 1 kg CaCO3 m−2 annum−1. Variation in food ingestion rates in response to seawater temperature changes was found to be the main driver for differences in seasonal bio-erosion rates, which likely contribute to the absence of macroalgae and the maintenance of high coral cover on Hall Bank Reef. This study provides baseline data on bio-erosion by a sea urchin at Hall Bank Reef, which will be essential in monitoring and managing reefs in this region, especially under current trends in climate change