This study evaluated the effect of the antero-posterior position of the midpalatal orthodontic mini-implant during maxillary posterior teeth intrusion using three-dimensional finite element model (3D-FEM) analysis. Methods A 3D-FEM was constructed from the computed tomography (CT) data of an adult male patient. Three simulation models were constructed according to the midpalatal mini-implant position: Model 1, at the interproximal level of the second premolar and first molar; Model 2, at the mesiopalatal cusp level of the first molar; and Model 3, at the interproximal level of the first and second molars. A 200-g force was applied from the bilateral hooks of the transpalatal arch (TPA) to the location of the mini-implant. Results In all models, the whole maxillary teeth showed intrusive movement, most at the second molar. As the mini-implant was positioned more posteriorly, intrusive displacement of the posterior teeth increased, while the intrusion and labioversion of the anterior teeth decreased. The palatal tipping movement of posterior teeth was remarkable. The highest stress value was shown on the trifurcation and palatal root surface area of the first molar. Conclusion A posteriorly positioned midpalatal mini-implant was more effective to intrude the maxillary posterior teeth without undesirable anterior teeth intrusion or labioversion. Expansion or buccal torque bending of the TPA could prevent the palatal tipping of the posterior teeth.