The purpose of this study was to analyse distal movements of molars in a force system using a trans-palatal arch (TPA), fixed to the maxillary first molar, and mini-implants placed at the palatal midline, considering the diagnostic standard for placement site in association with variation in upper molar locations, using finite element (FE) analysis. Three-dimensional FE models, divided by the differing direction of traction force, mesiodistal locations of the left and right molars, and the lateral location of the mini-implant were constructed. (1) When a traction force was fixed from the height of alveolar crest to the mini-implant placed at the middle of palate, the molars underwent bodily movement. (2) When the location of the mini-implant was moved to the left of the midline, the amount of distal movement of the left molar increased. When the mesiodistal locations of the left and right molars differed, the amount of distal movement of the molar located mesially was larger than that of the contralateral molar, even when the mini-implant was located on the midline.