The objective of this study was to investigate the effects of Pilates on pain, functional status, and quality of life in patients with ankylosing spondylitis. The study was performed as a randomized, prospective, controlled, and single-blind trial. Fifty-five participants (30 men, 25 women) who were under a regular follow-up protocol in our Rheumatology Clinic with the diagnosis of AS according to the modified New York criteria were included in the study. The participants were randomly assigned into two groups: in group I, Pilates exercise program of 1 h was given by a certified trainer to 30 participants 3 times a week for 12 weeks, and in group II, designed as the control group, 25 participants continued previous standard treatment programs. In groups, pre-(week 0) and post treatment (week 12 and week 24) evaluation was performed by one of the authors who was blind to the group allocation. Primary outcome measure was functional capacity. Evaluation was done using the Bath Ankylosing Spondylitis Functional Index (BASFI). Exploratory outcome measures were Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Bath Ankylosing Spondylitis Metrology Index (BASMI), Chest expansion, and ankylosing spondylitis quality of life (ASQOL) questionnaire. In group I, BASFI showed significant improvement at week 12 (P = 0.031) and week 24 (P = 0.007). In group II, this parameter was not found to have significantly changed at week 12 and week 24. Comparison of the groups showed significantly superior results for group I at week 24 (P = 0.023). We suggest Pilates exercises as an effective and safe method to improve physical capacity in AS patients. Our study is the first clinical study designed to investigate the role of Pilates method in AS treatment. We believe that further research with more participants and longer follow-up periods could help assess the therapeutic value of this popular physical exercise method in AS.