Objective To determine whether the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and the Ankylosing Spondylitis Disease Activity Score (ASDAS) exhibited differences between women and men. Methods We systematically searched MEDLINE, Embase, Web of Science and other sources in English or Spanish from 01 January 1995 to 31 July 2020, to assess the differences according to sex in BASDAI and ASDAS. We performed a comparative analysis by sex using t-student test and mean difference by sex meta-analyses for BASDAI and ASDAS, using a random-effects model via the inverse-variance method. Results Forty-one studies included BASDAI (6,785 women/12,929 men) and 16 of them included ASDAS (2,046 women/4,403 men). Disease activity detected through BASDAI was significantly higher in women than in men (mean: 4.9 vs. 4.2, p=0.02), whereas ASDAS did not detect differences between sexes (mean: 2.8 women vs. 2.8 men). In the meta-analyses, BASDAI detected significant differences between women and men [mean difference= 0.55 (95% confidence intervals (95%CI): 0.46, 0.65), p<0.00001], but ASDAS did not identify significant mean difference between sexes [0.04 (95%CI: -0.05, 0.12), p=0.38]. Conclusion The two most widely used indexes of disease activity in spondyloarthritis discriminate differently according to sex by their different evaluation of peripheral disease. Their different components and weights influence BASDAI and ASDAS values. BASDAI may be influenced by fatigue, but in predominantly peripheral manifestations like enthesitis, ASDAS may not be sensitive enough to detect activity. This may represent a gender bias unfavourable to women, because peripheral spondyloarthritis is more common in women than in men.