The purpose of this study is to understand the course of costs over a 2-year period in a cohort of recently diagnosed fibromyalgia (FM) patients receiving different treatment strategies. Following the diagnosis, patients were randomly assigned to a multidisciplinary programme (MD), aerobic exercise (AE) or usual care (UC) without being aware of alternative interventions. Time between diagnosis and start of treatment varied between patients. Resource utilisation, health care costs and costs for patients and families were collected through cost diaries. Mixed linear model analyses (MLM) examined the course of costs over time. Linear regression was used to explore predictors of health care costs in the post-intervention period. Two hundred three participants, 90 % women, mean (SD) age 41.7 (9.8) years, were included in the cohort. Intervention costs per patient varied from €864 to 1392 for MD and were €121 for AE. Health care costs (excluding intervention costs) decreased after diagnosis, but before the intervention in each group, and increased again afterwards to the level close to the diagnostic phase. In contrast, patient and family costs slightly increased over time in all groups without initial decrease immediately after diagnosis. Annualised health care costs post-intervention varied between €1872 and 2310 per patient and were predicted by worse functioning and high health care costs at diagnosis. In patients with FM, health care costs decreased following the diagnosis by a rheumatologist. Offering patients a specific intervention after diagnosis incurred substantial costs while having only marginal effects on costs.