Background <p>Subacute low back pain (LBP) is a critical phase that can determine long-term patient outcomes. Exercise therapy, including Pilates, is widely used to manage LBP, but its effectiveness in the subacute phase remains underexplored. This randomized controlled trial aims to compare the effects of an 8-week Pilates-based intervention versus a home exercise program on pain intensity, functional disability, and quality of life in patients with subacute LBP.</p> Methods <p>Sixty-six participants with subacute LBP were randomized into two groups: a supervised Pilates group and a home exercise group. Pain intensity (Visual Analog Scale), functional disability (Roland-Morris Disability Questionnaire), and quality of life (Short Form-36) were assessed at baseline, post-intervention, and 3-month follow-up.</p> Results <p>Both groups exhibited significant improvements in all outcome measures (<i>p</i> &lt; 0.001). However, the Pilates group showed superior reductions in pain intensity (<i>p</i> = 0.010 post-treatment, <i>p</i> = 0.002 at follow-up) and functional disability (<i>p</i> = 0.009 and <i>p</i> = 0.002). Additionally, quality of life scores improved more significantly in the Pilates group, particularly in physical function (<i>p</i> = 0.031 and <i>p</i> = 0.025) and general health (<i>p</i> = 0.005 and <i>p</i> = 0.012).</p> Conclusions <p>Pilates-based rehabilitation was more effective than a home exercise program in improving pain, disability, and quality of life in patients with subacute LBP. These findings support the inclusion of Pilates in early-stage rehabilitation to prevent chronicity.</p> Trial registration <p>Clinical Trials Number: NCT06699511.</p>