INTRODUCTION: Physical therapy in warm water has been effective and highly recommended for persons with fibromyalgia, but its efficiency remains largely unknown. Should patients or health care managers invest in this therapy? The aim of the current study was to assess the cost-utility of adding an aquatic exercise programme to the usual care of women with fibromyalgia. METHODS: Costs to the health care system and to society were considered in this study that included 33 participants, randomly assigned to the experimental group (n = 17) or a control group (n = 16). The intervention in the experimental group consisted of a 1-h, supervised, water-based exercise sessions, three times per week for 8 months. The main outcome measures were the health care costs and the number of quality-adjusted life-years (QALYs) using the time trade-off elicitation technique from the EuroQol EQ-5D instrument. Sensitivity analyses were performed for variations in staff salary, number of women attending sessions and time spent going to the pool. The cost effectiveness acceptability curves were created using a non-parametric bootstrap technique. RESULTS: The mean incremental treatment costs exceeded those for usual care per patient by euro 517 for health care costs and euro 1,032 for societal costs. The mean incremental QALY associated with the intervention was 0.131 (95% CI: 0.011 to 0.290). Each QALY gained in association with the exercise programme cost an additional euro 3,947/QALY (95% CI: 1,782 to 47,000) for a health care perspective and euro 7,878/QALY (3,559 to 93,818) from a societal perspective. The curves showed a 95% probability that the addition of the water-based programme is a cost-effective strategy if the ceiling of inversion is euro 14,200/QALY from a health care perspective and euro 28,300/QALY from a societal perspective. CONCLUSION: The addition of an aquatic exercise programme to the usual care regime for fibromyalgia in women is cost effective in terms of both health care costs and societal costs. However, the characteristics of facilities (distance from the patients' homes and number of patients that can be accommodated per session) are major determinants to consider before investing in such a programme. TRIAL REGISTRATION: Current controlled trials ISRCTN53367487.