Exercise has been shown to significantly improve pain and function in individuals with fibromyalgia. Research into the effectiveness of exercise is often based on standardised exercise programmes that are chosen by the investigating clinical research team. However, such programmes may not necessarily be appealing to the participating patients. Furthermore, in addition to being taught exercises, patients with chronic conditions like fibromyalgia also need to learn to manage their condition themselves and so be actively involved in their treatment. The primary aim of this study is to compare the effects of two, 6-month physical activity programs on quality of life in patients with fibromyalgia. One group followed a patient-led, fibromyalgia-orientated programme (experimental) whilst the control group followed a standard, general exercise programme. Methods This protocol is an open-label, two-centre, randomised, controlled superiority trial. Two treatment arms will be compared: an experimental group (patient-led, fibromyalgia-orientated exercise) and a control group (general exercise program). The control group will participate in the exercise programme currently provided in our centre, which involves general, group exercise for patients with various pathologies. The experimental group will be taught the principles of exercise specifically for fibromyalgia during a one-to-one coaching session. They will then be guided in the choice of one or several types of exercise that they enjoy. They will be instructed to perform the exercise according to the recommendations for exercise in fibromyalgia with regard to intensity, duration and frequency. The protocol will last for 6 months; participants will then be followed-up for a further 6 months. They will also be encouraged to continue exercising after the end of the protocol. Outcomes will be evaluated at baseline, 6 and 12 months. The primary outcome will be quality of life (Fibromyalgia Impact Questionnaire) and the secondary outcomes will include measures of pain (including a visual analogue scale and the neuropathic characteristics of the pain), depression (Hospital Anxiety and Depression Scale), kinesiophobia (Tampa scale of kinesiophobia) and adherence (Polar OH1 heart rate monitor). Discussion The results of this study will show if patient-led, fibromyalgia-orientated exercise is more effective than a general exercise programme on fibromyalgia-related outcomes, including quality of life, and on adherence to continued exercise. Trial registration ClinicalTrials.gov NCT03895086 . Registration no. 2018-A02881-54. Registered on 29 March 2019