Our aim was to analyse body core temperature and peripheral vascular microcirculation at skin hypothenar eminence of the hands and its relationship to symptoms in fibromyalgia syndrome (FMS). A total of 80 FMS women and 80 healthy women, matched on weight, were enrolled in this case-control study. Thermography and infrared thermometer were used for evaluating the hypothenar regions and core body temperature, respectively. The main outcome measures were pain pressure thresholds (PPTs) and clinical questionnaires. Significant associations were observed between overall impact [ = 0.033; 95% confidence interval (95%CI) = 0.003, 0.062; = 0.030], daytime dysfunction ( = 0.203; 95%CI = 0.011, 0.395; = 0.039) and reduced activity ( = 0.045; 95%CI = 0.005, 0.085; = 0.029) and core body temperature in FMS women. PPTs including greater trochanter dominant ( = 0.254; 95%CI = 0.003, 0.504; = 0.047), greater trochanter non-dominant ( = 0.650; 95%CI = 0.141, 1.159; = 0.013), as well as sleeping medication ( = -0.242; 95%CI = -0.471, -0.013; = 0.039) were also associated with hypothenar eminence temperature. Data highlighted that FMS women showed correlations among body core temperature and hand temperature with the clinical symptoms.