High-riding vertebral artery (HRVA) at C2 is more prevalent in patients with rheumatoid arthritis (RA) than in the general population, but its clinical significance remains unclear. Recent evidence in non-RA individuals suggests that unilateral HRVA may contribute to atlantoaxial joint degeneration (AAJD) through asymmetric mechanical stress. This study investigated whether unilateral HRVA is similarly associated with the progression of AAJD in RA. We retrospectively analyzed 336 RA patients from the single institutional cohort who underwent CT scans, including C1-C2, between 2011 and 2024. HRVA was defined as a C2 internal height < 2 mm and/or isthmus height < 5 mm. Morphological parameters (C1 lateral mass height, C1/2 coronal inclination, and C1/2 relative rotation angle) and AAJD grades were evaluated. Logistic regression was used to identify factors associated with moderate-to-severe AAJD (grade ≥ 2). HRVA was observed in 147 patients (116 unilateral). Compared with patients without HRVA, those with unilateral HRVA had longer RA duration (17.5 vs. 12.9 years, p < 0.01) and higher ACPA positivity (78.8% vs. 66.9%, p < 0.05), but no differences in disease activity or medication use. Moderate-to-severe AAJD was significantly more frequent in the unilateral HRVA group (62.9% vs. 42.3%, p < 0.001). Multivariate analysis identified older age, longer RA duration, and unilateral HRVA as independent risk factors for AAJD. These findings indicate that unilateral HRVA is independently associated with atlantoaxial facet joint degeneration in patients with RA in addition to aging and disease duration, suggesting a role of asymmetric mechanical loading in cervical joint pathology.