The percentage of spine misalignment increases during the childhood and adolescence stages. The Pilates method has been associated with an improvement in the sagittal spine disposition, but no studies have been conducted on adolescents. Therefore, the present study aimed to evaluate the effectiveness of a 9-month Pilates exercise program (PEP) on hamstring extensibility and sagittal spinal curvatures on adolescents. This randomised controlled trial included 236 adolescents. The experimental group (EG) received a PEP (9 months, 2 sessions/week, 15 minutes/session). The control group (CG) did not receive any intervention. Hamstring extensibility was measured with the passive and active straight leg raise and toe-touch tests. Sagittal spinal curvatures and pelvic tilt was assessed in relaxed standing, active alignment and toe-touch test positions. The EG had significant changes in hamstring extensibility, lumbar curvature and pelvic tilt in standing sagittal curvature. The CG became significantly worse in thoracic kyphosis in standing. This study provides evidence of nine-months of a PEP increased the hamstring extensibility; averted the increase of the thoracic curvature, and decreased the curvature of the lumbar lordosis and pelvic tilt in standing position; avoided a greater increase of thoracic curvature in active alignment in standing position; and avoided the increase of thoracic curvature in trunk flexion.