To compare the efficacy of intermittent and consecutive balneological outpatient treatment (hydrotherapy and peloidotherapy) in fibromyalgia syndrome (FMS). A parallel 1:1, single-blind, pilot study was performed. Patients were recruited from musculoskeletal disorders outpatient clinic. Eligible participants were patients aged 18-60, diagnosed as FMS according to ACR 2010 criteria. They were randomly assigned to either consecutive or intermittent treatment groups. Both groups received 20 min of full body immersion in a tap water pool at 38-39 °C and 30 min of mud pack application on the back region at 45 °C. Delivery of the treatment was five times weekly during 2 weeks in consecutive group and two times weekly during 5 weeks in intermittent group. The primary outcomes were pain intensity and the number of patients achieving a minimal clinically important difference (MCID) on Fibromyalgia Impact Questionnaire (FIQ) at the 1st month after the completion of the treatment. Statistical analyses were based on intention to treat method. The assessing physician was blinded. Pain intensity significantly decreased in all post-treatment evaluations of both groups (except after treatment in the intermittent group). There was no significant difference between the groups. MCID for FIQ was achieved in 6 (24%) patients in the consecutive group and 12 (48%) in the intermittent group at the 1st month. There was no statistical difference in the secondary judgment criteria. The consecutive and intermittent deliveries of balneological outpatient treatment (hydrotherapy and peloidotherapy) seem to have similar effects on the clinical status of patients with FMS.