Resorption within cortices of long bones removes excess mass and damaged tissue, and increases during periods of reduced mechanical loading. Returning to high-intensity exercise may place bones at risk of failure due to increased porosity caused by bone resorption. We used microradiographic images of bone slices from highly-loaded (metacarpal, tibia, humerus) and minimally-loaded (rib) bones from 12 racehorses, 6 in active high-intensity exercise and 6 in a period of rest following intense exercise, and measured intracortical canal cross-sectional area (Ca.Ar) and number (N.Ca) to infer remodelling activity across sites and exercise groups. Large canals representing resorption spaces (Ca.Ar > 0.04 mm2) were 5- to 18-fold greater in number and area in the third metacarpal bone from rested than exercised animals (p = 0.005–0.008), but were similar in number and area in ribs from rested and exercised animals (p = 0.575–0.688). A weaker, intermediate relationship was present in tibia and humerus, and when resorption spaces and partially-infilled canals (Ca.Ar > 0.002 mm2) were considered together. The mechanostat may override targeted remodelling during periods of high mechanical load by enhancing bone formation, reducing resorption and suppressing turnover, but both systems may work synergistically in rest periods to remove excess and damaged tissue.