Ureteral peristalsis can be considered as a series of waves on the ureteral wall, which transfers the urine along the ureter toward the bladder. The stones that form in the kidney and migrate to the ureter can create a substantial health problem due to the pain caused by interaction of the ureteral walls and stones during the peristaltic motion. Three-dimensional (3D) computational fluid dynamics (CFD) simulations were carried out using the commercial code ansys fluent to solve for the peristaltic movement of the ureter, with and without stones. The effect of stone size was considered through the investigation of varying obstructions of 5%, 15%, and 35% for fixed spherical stone shape. Also, an understanding of the effect of stone shape was obtained through separate CFD calculations of the peristaltic ureter with three different types of stones, a sphere, a cube, and a star, all at a fixed obstruction percentage of 15%. Velocity vectors, mass flow rates, pressure gradients, and wall shear stresses were analyzed along one bolus of urine during peristalsis of the ureteral wall to study the various effects. It was found that the increase in obstruction increased the backflow, pressure gradients, and wall shear stresses proximal to the stone. On the other hand, with regard to the stone shape study, while the cube-shaped stones resulted in the largest backflow, the star-shaped stone showed highest pressure gradient magnitudes. Interestingly, the change in stone shape did not have a significant effect on the wall shear stress at the obstruction level studied here.