The aim of this study was to identify exercise-related risk factors for carpal and metacarpo- and metatarso-phalangeal (MCP/MTP) joint injury occurrence in young Thoroughbreds in flat race training. In a 2-year prospective cohort study, daily exercise and joint injury data were collected from horses in 13 training yards in England. Four injury categories were defined: (1) localised to a carpal or MCP/MTP joint based on clinical examination and/or use of diagnostic analgesia with no diagnostic imaging performed; (2) localised to a carpal or MCP/MTP joint with no abnormalities detected on diagnostic images; (3) abnormality of subchondral bone and/or articular margin(s) identified using diagnostic imaging; (4) fracture or fragmentation identified by diagnostic imaging. Multivariable Cox regression analysis was conducted to determine risk factors for injury occurrence, by type (carpal or MCP/MTP) and category. Exercise distances at canter and high speed in different time periods were modelled as continuous time-varying variables. A total of 647 horses spent 7785months at risk of joint injury and 184 injuries were recorded. Increasing daily canter distance reduced the risk of Category 1 and Category 3 injuries whereas greater 30-day canter distances increased Category 4 injury risk. More weekly high-speed exercise increased Category 1 injury risk. MCP/MTP injury risk reduced with increasing daily canter distance but increased with accumulation of canter or high-speed exercise since entering training, whereas accumulation of canter exercise was marginally associated with reduced carpal injury risk. Risk of all injury types varied significantly between trainers. The results of this study suggest that regular canter exercise is generally beneficial for joint health, while accumulation of high-speed exercise detrimentally affects MCP/MTP joints.