Introduction: Fatigue is frequent in long-standing axial spondyloarthritis (axSpA); its frequency in early axSpA and its causes are unclear. The objective was to evaluate the magnitude of fatigue in early axSpA and to assess if fatigue appeared more strongly associated with patient- or with disease-related characteristics. Methods: Patients were assessed in DESIR, a national observational cohort of patients with recent (< 3 years duration) inflammatory back pain suggestive of axSpA. Magnitude of fatigue was assessed by a numeric rating scale (0–10) over one year. Factors associated with high fatigue ( ≥ 5/10) at 12 months were assessed by univariate and multivariate logistic regression, for patients fulfilling the ASAS axSpA criteria. Results: Of the 708 patients, 486 fulfilled the ASAS criteria for axSpA: mean age 33 ± 9 years; 244 (50%) males. Magnitude of fatigue was high at baseline (mean fatigue: 5.7 ± 2.3) and decreased only slightly over the first year, and was overlapping in patients fulfilling the ASAS criteria or not. High fatigue at 12 months was well explained (variance explained: 0.84) by a higher ASDAS-CRP (odds ratio [OR]: 3.05 [95% confidence interval (CI) 2.27–4.12], P < 0.0001), higher Bath Anylosing Spondylitis Patient Global (BAS-G) (OR: 3.51 [95% CI, 2.08–6.02], P < 0.0001) and with borderline significance, female gender (OR: 1.65 [95% CI, 1.00–2.71], P = 0.049). Conclusion:Fatigue levels were high in this population, both for patients fulfilling or not, the ASAS criteria for axSpA. High fatigue was closely related to disease-related variables, indicating fatigue may be an integral part of the disease process in axSpA.