To assess the effectiveness of 12 weeks of Pilates practice on disability, pain and kinesiophobia in patients with chronic non-specific low back pain. This is a randomized controlled trial. This study was conducted in the university laboratory. A total of 64 participants with chronic non-specific low back pain were included. Participants were randomly allocated to intervention group consisted in Pilates intervention during 12 weeks (n = 32) or control group who received no treatment (n = 32). Disability, pain and kinesiophobia were assessed by Roland Morris Disability Questionnaire, visual analogue scale and Tampa Scale of Kinesiophobia, respectively. Measurements were performed at baseline, at 6 and 12 weeks after study completion. There were significant differences between groups with observed improvement in Pilates intervention group in all variables after treatment (P < 0.001). Major changes on disability and kinesiophobia were observed at six weeks of intervention with no significant difference after 12 weeks (P < 0.001). Mean changes of the intervention group compared with the control group were 4.00 (0.45) on the Roland Morris Disability Questionnaire and 5.50 (0.67) in the Tampa Scale of Kinesiophobia. Pain showed better results at six weeks with a slightly but statistically significant improvement at 12 weeks with Visual Analogue Scale scores of 2.40 (0.26) (P < 0.001). Pilates intervention in patients with chronic non-specific low back pain is effective in the management of disability, pain and kinesiophobia.