The aim of the study was to determine whether the Functional Movement Screen (FMS) test carried out among young boys practising football training identifies previous injuries. Sixty-five boys aged 12–13 years, who had regularly practised football in an academy for at least 3 years, were recruited and divided into two groups: an injured group (IG), consisting of players who had experienced at least one injury in the past (n + 25, age 12.32 ± 0.48) and a non-injured group (non-IG), a control group, made up of athletes with no injuries to the musculoskeletal system (n = 40, age 12.25 ± 0.49). Seven FMS tests were used to rate the functional fitness level as a part of the FMS tool. Significant differences between the total scores of the FMS tests (p < 0.001, r = 0.54) were documented. Higher scores in the FMS test were observed in the control group (M = 16.58, SD = 2.04) than in the study group (M = 14.20, ± SD = 1.96). The FMS test is an effective diagnostic tool to identify previous injuries among young football players.