Background—Upper molar distalization with a clear aligner is a debated topic in the scientific literature. One of the main issues is the loss of anchorage, so Class II elastics or the application of miniscrews are recommended. The aim of this study is to evaluate, through Finite Element Method (FEM) analysis, the effects of the application of the interradicular miniscrew as an anchorage device. Methods—A maxillary arch model from the second molar to second molar, which was obtained from a Cone Beam Computed Tomography (CBCT) and 0.2 mm distalization of the upper second premolar and upper first molar, was simulated. Therefore, nine different anchorage configurations were analyzed, with a miniscrew simulated between the upper first and second molars. Results—Considering the anchorage of a Class I elastic on the first premolar, the resulting side effect was a buccal movement of the canine. When the Class I elastic was anchored on the canine, distal displacement of the canine was observed. The distalization movements of second premolars and first molars were more efficient when the elastics were parallel to the occlusal plane. A greater anterior anchorage loss was observed when the elastic was anchored on the canine, with a proclination of the upper central incisor 30% higher than in the simulation, in which the elastic was on the first premolar. Conclusion—The use of interradicular buccal skeletal anchorage could reduce issues of patient compliance, provide a consistent intraoral anchorage unit and allow the desired tooth movements, reducing unwanted movement of the anterior teeth.