IntroductionFibromyalgia syndrome (FMS) imposes a high cost on society. The significant economic burden from the use of healthcare and, especially, social resources is a spur to revising the usual clinical care (UCC) and to improving treatment strategies. FMS has a deleterious effect on the quality of life (QOL) and productivity, which considerably increase the indirect costs to society. This study reports an economic evaluation comparing the cost and health benefits in a multicomponent intervention programme and UCC of patients with FMS who attend primary healthcare centres of the Gerència Territorial Terres de L’Ebre region of Catalonia, Spain. This article is linked to the pre-results of a randomised control trial study on the implementation of this intervention programme (ClinicalTrials.gov: NCT04049006).Method and analysisA cost–utility analysis will be conducted from a societal perspective. Quality-adjusted life years will be calculated from the results of the SF-36 questionnaire, a QOL measurement instrument. Direct and indirect healthcare costs will be obtained from official prices and reports published by the Spanish Public Health Administration and the National Statistics Institute. The incremental cost–utility ratio will be estimated to compare the two healthcare practices. Deterministic sensitivity analysis will also be used to compare different cost scenarios, modifying the items with the highest weight in the cost composition.Ethics and disseminationThe Clinical Research Ethics Committee of the IDIAPJGol Institute approved this study on 25 April 2018 (code P18/068) in accordance with the Helsinki/Tokyo Declaration. Information will be provided orally and in writing to participants, and their informed consent will be required. Participant anonymity will be guaranteed. The dissemination strategy includes publications in scientific journals and presentations in local and national media and at academic conferences.Trial registration number:NCT04049006; Pre-results.