Climate change driven increases in intensity and frequency of both hot and cold extreme events contribute to coral reef decline by causing widespread coral bleaching and mortality. Here, we show that hot and cold temperature changes cause distinct physiological responses on different time scales in reef-building corals. We exposed the branching coral Acropora yongei in individual aquaria to a ± 5°C temperature change. Compared to heat-treated corals, cold-treated corals initially show greater declines in growth and increases in photosynthetic pressure. However, after 2–3 weeks, cold-treated corals acclimate and show improvements in physiological state. In contrast, heat did not initially harm photochemical efficiency, but after a delay, photosynthetic pressure increased rapidly and corals experienced severe bleaching and cessation of growth. These results suggest that short-term cold temperature is more damaging for branching corals than short-term warm temperature, whereas long-term elevated temperature is more harmful than long-term depressed temperature.