The objective of this study was to compare the effect of aerobic and balance exercises on pain intensity, myalgic score, quality of life, exercise capacity and balance in fibromyalgia syndrome (FMS). In all, 33 females diagnosed with FMS by the American College of Rheumatology criteria were recruited in this randomised controlled study and allocated to aerobic exercise (AE) or balance exercise (BE) groups. Exercises were performed three times a week, for 6 weeks on a treadmill or with a Tetrax interactive balance system (TIBS). Outcome measures were characterised by myalgic score, visual analogue scale, Fibromyalgia Impact Questionnaire (FIQ), exercise testing, Timed Up-Go (TUG) and TIBS measurements. Comparisons from baseline to 6 weeks were evaluated using Wilcoxon test. Mann-Whitney U test was used to compare differences between groups. Effect sizes were also calculated. Improvements in pain, myalgic score and FIQ were found in both groups (p<0.05). While comparing groups, myalgic score was significant (p=0.02, d=-1.77), the value was higher in AE. Exercise duration, Borg scale, resting blood pressures (RBP) and maximal heart rate were significant in AE. In BE, Borg scale, exercise duration was significant (p<0.05). In the process of comparing groups, diastolic RBP (p=0.04, d=-0.92), exercise duration (p=0.00, d=-1.64) were significant, with higher values in AE. TUG significantly altered in groups (p-1.22). Stability scores, eyes open while standing on elastic pads (p=.00, d=-0.98) and head back (p=0.03, d=-0.74), were significant, with higher values in BE. This study revealed that BE resulted in some improvements in FMS, but AE training yielded greater gains. BE training should be included in comprehensive programs.