Magnetic resonance (MR) imaging-based disease activity scores (DAS) in axial spondyloarthritis (axSpA) are rarely employed in the normal clinical setting, whereas clinical DAS are used routinely to monitor disease activity and set thresholds for biologic treatment. The objectives of this study were to evaluate the correlation between MR and clinical DAS in a general axSpA outpatient population and to assess the difference in MR DAS in individuals with high and low clinical DAS. This was a prospective, cross-sectional observational study. Forty participants with axSpA who presented for MR of the whole spine and sacroiliac joints as part of ongoing management were included. Completion of Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) and Ankylosing Spondylitis Disease Activity Score (ASDAS) was performed at the time of MR examination. MR images were scored by two independent observers using the Spondyloarthritis Research Consortium of Canada (SPARCC) MR DAS. There were weak, non-significant correlations between total SPARCC score and BASDAI (r = 0.18, p = 0.26), ASDAS using erythrocyte sedimentation rate (ASDAS-ESR) (r = 0.31, p = 0.07) and ASDAS using C-reactive protein level (ASDAS-CRP) (r = 0.31, p = 0.05). There was no significant difference in the SPARCC score of participants with high and low clinical DAS. MR DAS may provide information about disease activity not provided by the current standard of clinical DAS and may be considered as a useful adjunct in clinical practice.