The aims of this study were to analyze the muscle injury incidence in an elite Spanish soccer academy during three consecutive seasons attending to different chronological age groups (i.e., U14, U16, U19 and senior) and to examine the hamstring injury incidence in this elite soccer academy. Elite male youth soccer players (227) participated in this study. A total of 207 time-loss injuries (i.e., injuries that involve at least one absence day) were observed during this study period. The overall incidence rate of muscle injury was 1.74 muscle injuries/1000 h. In addition, higher muscle injury incidence was observed during match play in comparison to training sessions (6.78 vs. 3.20 muscle injuries/1000 h, p < 0.05). The oldest age group presented the highest injury rate (2.73 muscle injuries/1000 h, p < 0.05), with the burden (i.e., number of absence days per 1000 h of exposure) peak values recorded in the U16 age group (26.45 absence days/1000 h). In addition, muscle tears accounted for the greatest percentage of muscle injuries (43.5%), and the most frequent anatomical site of injury was the hamstring (30.4%). Muscle tear was the most common type of hamstring injury (49.2%), with the biceps femoris the most commonly injured muscle of the hamstring complex (39.7%). Fullbacks (FB), wide midfielders (WM) and forwards (F) suffered a greater number of hamstring injuries. Hamstring injury incidence showed a seasonal variation, as indicated by peaks in August and October. Specifically, the highest injury incidence was observed in the final part of each period during match play. These results reinforce the necessity to implement individual preventive strategies according to each specific injury profile across the youth soccer development phase.