Background Spinal manipulative therapy is commonly used in the treatment of adolescent idiopathic scoliosis. Some therapists also rely on physiotherapeutic scoliosis-specific exercise (PSSE). Combining these two modalities seems reasonable, but the effectiveness of this combination has never been rigorously tested. Here, a protocol for a pilot study is proposed to determine the feasibility of conducting a larger randomized trial. The pilot study was designed to test the hypothesis that spinal manipulative therapy followed by PSSE is more effective than PSSE alone in improving the Cobb angle, sensorimotor integration, the angle of trunk rotation (ATR), body symmetry, and quality of life. Methods The protocol describes a randomized controlled pilot trial with 40 subjects divided into study and control groups. Both groups will receive 8 weeks of PSSE, but the study group will also receive spinal manipulative therapy during the first 2 weeks before PSSE. The primary outcome will be an estimate of the feasibility of conducting a full-scale experiment. The influencing factors will be the time to complete enrollment, the recruitment rate, subject retention, and adherence to the treatment allocations. The secondary outcomes that will be used to assess the efficacy of treatment will include the Cobb angle, somatosensory evoked potentials, ATR, three-dimensional postural parameters, and scores on the 22-item Scoliosis Research Society outcomes questionnaire. The Cobb angle will be measured at baseline and at the end of 8 weeks of training. The somatosensory evoked potentials will be measured at baseline and at the end of 2 weeks of training. The ATR, three-dimensional postural parameters, and scores on the 22-item Scoliosis Research Society outcomes questionnaire will be measured at baseline and at 2 weeks, 4 weeks, and 8 weeks of treatment. Discussion This study will inform the design of a future full-scale trial. The outcomes will provide preliminary data about the efficacy of the combination of spinal manipulative therapy and exercise in treating scoliosis.