The aim of this study was to describe the epidemiology of elite youth soccer knee injuries from prospective data collected from forty-one English FA Football Academies over a 5 year period. 12306 players were registered from U9 to the U16 age category. We studied the incidence of injuries around the knee with particular emphasis upon those causing greater than 28 days time off sport. There were 609 knee injuries with a mean incidence of 0.71 knee injuries per player per year and a median of 17 training days and 2 matches missed per knee injury. Increased injury rates were seen in older players, in competitive situations and in the latter stages of each half of play. Peaks in injury numbers were seen in early season and subsequent to the winter break. Sprain was the most common diagnosis with the Medial Collateral ligament affected in 23.2% of cases. 609 injuries met the UEFA Model criteria for major injury. In total 60,091 training days and 5,272 match appearances were lost through knee injury. Knee injuries are common in elite level youth footballers and are often severe in nature, resulting in large amounts of training time lost to injury. Diagnosis of ligament sprain is common leading to prolonged time off, and may mask more serious pathology or inappropriate management.