Cortical bone thickness is assumed to be a major factor regulating miniscrew stability. We investigated stress distribution in two miniscrews with different thread shapes (type A and B) and in cortical bone of three different thicknesses using three-dimensional (3D) finite element (FE) models. More specifically, 3D FE models of two different miniscrews were created and placed obliquely or vertically into a cylindrical bone model representing different cortical bone thicknesses. When force was applied to the miniscrew, the stress distribution on the screw surface and in the peri-implant bone was assessed using FE methodology. Miniscrew safety was evaluated using a modified Soderberg safety factor. Screw head displacement increased with a decrease in cortical bone thickness, irrespective of screw type. The smallest minimum principal stresses on the screw surfaces remained constant in type A miniscrews on changes in cortical bone thickness. Minimum principal stresses also appeared on the cortical bone surface. Lower absolute values of minimum principal stresses were seen in type A miniscrews when placed vertically and with upward traction in obliquely placed type B miniscrews. Both miniscrews had acceptable safety factor values. Taken together, orthodontists should select and use the suitable miniscrew for each patient in consideration of bone properties.