PurposeActivated brown adipose tissue (BAT) enhances lipid catabolism and improves cardiometabolic health. Quantitative MRI of the fat fraction (FF) of supraclavicular BAT (scBAT) is a promising noninvasive measure to assess BAT activity but suffers from high scan variability. We aimed to test the effects of coregistration and mutual thresholding on the scan variability in a fast (1 min) time‐resolution MRI protocol for assessing scBAT FF changes during cold exposure.MethodsTen volunteers (age 24.8 ± 3.0 years; body mass index 21.2 ± 2.1 kg/m2) were scanned during thermoneutrality (32°C; 10 min) and mild cold exposure (18°C; 60 min) using a 12‐point gradient‐echo sequence (70 consecutive scans with breath‐holds, 1.03 min per dynamic).Dynamics were coregistered to the first thermoneutral scan, which enabled drawing of single regions of interest in the scBAT depot. Voxel‐wise FF changes were calculated at each time point and averaged across regions of interest. We applied mutual FF thresholding, in which voxels were included if their FF was greater than 30% FF in the reference scan and the registered dynamic. The efficacy of the coregistration was determined by using a moving average and comparing the mean squared error of residuals between registered and nonregistered data. Registered scBAT ΔFF was compared with single‐scan thresholding using the moving average method.ResultsRegistered scBAT ΔFF had lower mean square error values than nonregistered data (0.07 ± 0.05% vs. 0.16 ± 0.14%; p < 0.05), and mutual thresholding reduced the scBAT ΔFF variability by 30%.ConclusionWe demonstrate that coregistration and mutual thresholding improve stability of the data 2‐fold, enabling assessment of small changes in FF following cold exposure.