ObjectiveThe objective was to determine sex differences in disease outcomes in recent axial spondyloarthritis (SpA) over time.MethodsWe analyzed the first 6 years of follow‐up of the prospective French multicenter DESIR cohort. Patients analyzed had <3 years of disease, were naive to disease‐modifying antirheumatic drugs, and fulfilled the Assessment of SpondyloArthritis international Society classification criteria for axial SpA. Disease activity (Ankylosing Spondylitis Disease Activity Score [ASDAS] using the C‐reactive protein [CRP] level), patient global assessment (PtGA), CRP level, and radiographic sacroiliitis were compared between men and women (self‐reported sex) by linear and logistic mixed‐effects models. Models were created for trajectories of disease activity over 6 years in men and women, using k‐means.ResultsOf 494 patients analyzed (mean ± SD age 31.9 ± 7.5 years, symptoms duration 20.7 ± 11.7 months), 50.4% were men. Over 6 years of follow‐up, both men and women showed clear improvements in ASDAS‐CRP, PtGA, and CRP level. Women had higher ASDAS‐CRP and PtGA over time compared to men (both P < 0.0001) with overall similar CRP levels (P = 0.089), whereas structural damage increased more in men (P < 0.0001). One‐third of both men (33%) and women (34%) belonged to persistent high/very high disease activity trajectories, but ASDAS‐CRP was globally higher in women in these trajectories.ConclusionIn early axial SpA, clinical outcomes (disease activity and symptoms) were worse in women than men over 6 years of follow‐up, whereas CRP was similar and structural damage was more frequent in men. Although similarly distributed, disease activity scores were higher in women in high/very high disease activity trajectories. Sex appears to be an important contextual factor in axial SpA.image