Accurate bracket placement is essential for successful orthodontic treatment. An indirect bracket bonding system (IDBS) has been developed to ensure proper bracket positioning with three-dimensional computer-aided transfer jigs. The purpose of this study was to investigate the accuracy of bracket positioning by a one-body transfer jig according to the tooth type and presence/absence of a resin base. In total, 506 teeth from 20 orthodontic patients were included in this study. After initial dental models were scanned, virtual setup and bracket positioning procedures were performed with 3D software. Transfer jigs and RP models were fabricated with a 3D printer, and brackets were bonded to the RP model with or without resin base fabrication. The best-fit method of 3D digital superimposition was used to evaluate the lineal and angular accuracy of the actual bracket position compared to a virtual bracket position. Although all the measurements showed significant differences in position, they were clinically acceptable. Regarding the tooth types, premolars and molars showed higher accuracy than anterior teeth. The presence or absence of a resin base did not consistently affect the accuracy. In conclusion, the proper application of IDBS should be performed considering the errors, and resin base fabrication might not be essential in ensuring high-accuracy IDBS.