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Background Injuries among youth athletes competing at an elite level are common. However, few studies have examined how training load, pain, and well-being develop in the weeks leading up to an injury. Understanding these factors may help in early identification and prevention of injuries.Methods In a prospective cohort study, 171 elite youth athletes were followed weekly and completed digital questionnaires reporting training load (session Rating of Perceived Exertion (sRPE)), pain (Numeric Rating Scale, (NRS)), well-being and injuries. Athletes who sustained an injury were compared to injury-free athletes by analyzing the four weeks preceding injury (weeks -1, -2, -3, and -4) against corresponding four-week intervals from injury-free individuals. The sRPE was analyzed using independent t-tests, while NRS and wellness were compared using Mann–Whitney U-tests.Results Athletes who sustained an injury reported significantly higher pain levels (NRS) in all four weeks prior to injury (p < 0.001). They also showed significantly lower training load (sRPE) one and two weeks before injury (p < 0.05), and significantly lower wellness scores during the three weeks prior to injury (p < 0.05). These patterns were not observed in the non-injured group.Conclusion The findings support the theory that injuries develop progressively, with increasing pain and declining well-being appearing before the injury occurs. The observed reduction in perceived training load may reflect a compensatory response to pain. Regular monitoring of pain, training load, and wellness could be valuable in identifying athletes at risk and enabling early intervention.