In the process of orthodontic treatment, root parallelism is related to the relapse of extraction spaces, black triangles, and periodontal health. However, there are few studies on root parallelism in extraction cases with different types of appliances. The objective was to compare the root parallelism in extraction cases treated with clear aligners vs. those treated with fixed appliances by measuring the differences per extraction site and to access the root-movement control capacity of both orthodontic appliances. A retrospective study was conducted on cases in which the first premolars were extracted, treated by clear aligner appliance (“Invisalign” system, 28 patients) or fixed appliance (30 patients). The angulations of the tooth axis (canines, the second premolars, the first molars, and the second molars) were measured to analyze and compare the difference in root parallelism between the two orthodontic appliances. The percentage of root parallelism between the canine and second premolar in both groups had no significant difference. However, judging from the average angle difference value, the fixed appliance might have a greater range in root angulation adjustment than the aligner. In the angulation categories, the aligner mainly showed root apical divergence, while the fixed appliance mainly showed root apical convergence. The dental crown of the molars was mainly non-tipping in both groups, but it could be observed that the dental crown of the maxillary molars had a tendency toward mesial inclination. In conclusion, the same root parallelism and root inclination were obtained in tooth extraction cases whether treated by clear aligners or fixed appliances. This study provides clinicians with more information on the performance of clear aligners and fixed appliances.