Soccer is a sport with worldwide popularity but has a substantial risk of injury. Clinical screening tools are an important factor in strategies of injury prevention. The purpose of the study was to examine the relationship between the Star Excursion Balance Test (SEBT) and injury and lower back pain (LBP) in amateur soccer players. The research was performed as a longitudinal cohort study on 42 amateur male soccer players with 15.8 ± 6.6 years of soccer playing (age: 25.5 ± 6 years). Participants were surveyed with regard to their soccer playing, injuries, and LBP, and the SEBT was performed. They were followed for 3.5 months. At the follow-up, an additional set of data regarding injuries and LBP was gathered. Significant differences were found in all directions and in the composite score of the SEBT between uninjured and injured players. Shorter distance in all directions and a lower composite score were associated with injury in general. Shorter distances in all but the anterior direction and a lower composite score were associated with lower extremity injury, and shorter anterior distance was associated with LBP. Amateur soccer players with lower SEBT scores are more prone to injuries in general, as well as injuries of the lower extremities. SEBT presents as a useful clinical screening tool in identifying amateur soccer players at risk of injury.