Purpose To investigate the prevalence of and factors associated with dysfunctional low back pain (LBP) in patients with rheumatoid arthritis (RA). Methods This cross-sectional study included 1276 RA outpatients from two hospitals. The Roland-Morris Disability Questionnaire was used to address the functional-dysfunctional state criterion. Clinical variables, such as medical status, disease activity, bone mineral density, and spinopelvic alignment parameters, were compared between patients with and without dysfunctional LBP. Results Mean age and disease duration were 64.6 and 13.4 years, respectively; the prevalence of dysfunctional LBP was 32.8%. On univariate analysis, significant differences existed in many variables, except sex, body weight, C-reactive protein (CRP) level, and prevalence of biological agent users, between patients with and without dysfunctional LBP. Multivariate logistic regression analysis revealed body mass index (BMI; odds ratio [OR], 1.116; P < 0.001), onset age of RA (OR, 1.020; P = 0.020), disease duration of RA (OR, 1.043; P < 0.001), methotrexate (MTX) use (OR, 0.609; P = 0.007), vertebral fractures (OR, 2.189; P = 0.001), vertebral endplate and/or facet erosion (OR, 1.411; P = 0.043), disease activity score (DAS) in 28 joints-CRP (DAS-28CRP) (OR, 1.587; P = 0.001), pelvic tilt (PT; OR, 1.023; P = 0.019), and sagittal vertical axis (SVA; OR, 1.007; P = 0.043) as associated factors. Conclusion The factors associated with dysfunctional LBP in patients with RA were more vertebral fractures, higher DAS-28CRP, vertebral endplate and/or facet erosion, higher BMI, longer disease duration, greater PT, older onset age, greater SVA, and less MTX use. Strictly controlling patients' body weight and disease activity with MTX and avoiding spinopelvic malalignment through vertebral fracture prevention are important.