Objective: The aim of this study was to evaluate the effects of the Pilates method on the reduction of pain, improvement of joint function, and quality of life of patients with chronic Chikungunya fever. Design: This is a randomized, controlled, blind trial for the evaluators. Setting: The study was conducted at the Advanced Laboratory in Physical Education and Health at Federal University of Pernambuco, Brazil. Subjects: A total of 51 patients were allocated randomly and divided into 2 groups: a Pilates group (26 patients) and a control group (25 patients). After 12 weeks, 4 patients in the Pilates group and 5 in the control group were lost to follow-up. Intervention: The Pilates group performed 24 Pilates method intervention sessions; the control group continued to receive standard clinical treatment at the outpatient clinic. Main measures: The main measures were as follows: visual analogue scale (VAS) for pain, functional capacity evaluated by Health Assessment Questionaire (HAQ), quality of life measured by the 12-Item Short-Form Health Survey (SF-12), and range of joint motion by goniometry. Results: After 12 weeks, patients in the Pilates group presented lower VAS ( P < 0.001), lower HAQ scores ( P < 0.001), and higher quality-of-life scores ( P < 0.001) compared with the control group. We found statistically significant results for the Pilates group in the range of movement for shoulder, knee, ankle, and lumbar spine ( P < 0.001). In the intragroup analysis, there was a significant improvement in all outcomes evaluated. Conclusion: In this study, patients undertaking Pilates method for 12 weeks had less pain, better function and quality of life, and increased range of joint movement.