Objective This study aimed to analyze the effect of changing various parameters of the bone-borne rapid palatal expander (RPE) using the finite element method (FEM). Methods In eight experimental groups, we investigated the effect of the number, position, and length of miniscrews; positional changes of the expander; and changes in the hook length on maxillary expansion. In finite element analysis, we compared the magnitude and distribution of stress, and the displacement changes following expansion of the bone-borne RPE. Results When we compared the number and position of miniscrews, placing miniscrews in the anterior and posterior sides was advantageous for maxillary expansion in terms of stress distribution and displacement changes. Miniscrew length did not significantly affect stress distribution and displacement changes. Furthermore, anteroposterior displacement of the expander did not significantly affect transverse maxillary expansion but had various effects on vertical changes of the maxilla. The maxilla rotated clockwise when the miniscrews were placed in the anterior region. The hook length of the expander did not show consistent results in terms of changes in stress distribution and magnitude or in displacement changes. Conclusions The findings of this study suggest that changes in the location and length of the miniscrews and displacement of the bone-borne RPE could affect the pattern of the maxillary expansion, depending on the combination of these factors.