Despite the well documented benefits of physical fitness (PF) on general health, its role in back pain (BP) is still unclear. The objective of this study was to assess the association between different PF profiles and BP in a sample of adolescents. The study assessed PF and BP in a sample of 919 youth (age = 15.5 ± 1.3 years) from North and South Tyrol. A total of 531 participants (57.8%) reported no BP, whereas 4.7% (n = 43) reported severe BP. A two-step cluster analysis detected three main groups: the “less fit”, with significantly lower scores in all PF tests (p < 0.001); the “strong sprinters”, with higher speed and muscular strength than the others (p < 0.001); and the “flexible marathoners”, with higher flexibility and cardiorespiratory fitness (p < 0.001). The “flexible marathoners” showed significantly better BP scores than the “less fit” (p = 0.029). Cardiorespiratory fitness and trunk flexibility are potential preventive components of BP in adolescents. Since the decline in flexibility starts very early in life, it is recommended to put a particular emphasis on this component of PF. The role of other components of PF should be further investigated in the future.