Background: Deep bite is known as one of the most common malocclusions, and its treatment and retention are often challenging. The use of mini-screws has been suggested as an ideal method for the intrusion of incisors in deep-bite patients. Still, there are conflicting reports regarding the superiority of this method compared to other common treatments. Aim: The aim of this systematic review and meta-analysis was to evaluate the effects of the intrusion of anterior teeth by skeletal anchorage in deep bite patients. Methods: From the beginning to 15 September 2022, articles on the topic of interest were searched in electronic databases including PubMed, Web of Science, Scopus, EMBASE, and Cochrane’s CENTRAL. Additionally, a hand search for pertinent studies and a search of the grey literature were carried out. After the selection of eligible studies, data extraction was performed using piloted forms. Inverse-variance random-effects meta-analyses were used to combine the outcome measures of dental indices, skeletal cephalometric indices, and dental cephalometric indices. Results: A total of 15 studies (6 RCT; 9 CCT) were included in the systematic review and 14 were used in the meta-analyses. The differences in overbite changes (MD = −0.45, p = 0.04), true incisor intrusion [u1-pp] (MD = −0.62, p = 0.003) and molar extrusion [u6-pp] (MD = −0.40, p = 0.01) were statistically significant and TADs showed better treatment results than other intrusion methods (segmented intrusion arch, utility arch, J hook headgear). No significant differences regarding overjet, molar and incisor tipping, and skeletal indices between mini-screw and other intrusion methods could be found. Conclusion: The use of mini-screws leads to lower overbite and higher true intrusion (about 0.45 and 0.62 mm, respectively) compared to the use of other methods for intruding upper incisors. Furthermore, the effect of TAD on extrusion of molar teeth is less (by 0.4 mm) than other methods.