Two common abnormalities in ureters include primary refluxing megaureter (PRM) and primary obstructed megaureter (POM). The aim of this study was to represent the numerical simulation of the urine flow at the end of the ureter with vesicoureteral reflux (VUR) and POM during peristalsis. Methodologically, the peristalsis in the ureter wall was created using Gaussian distribution. Fluid-structure interaction (FSI) was applied to simulate urine-elastic wall interactions; and governing equations were solved using the arbitrary Lagrangian-Eulerian method. Theories such as wall elasticity, Newtonian fluid, and incompressible Navier-Stokes equations were used. Velocity fields, viscous stresses and volumetric outflow rate profiles were obtained through the simulation of the ureter with VUR and POM during peristalsis. In addition, the effect of urine viscosity on flow rate was investigated. When the bladder pressure increased, VUR occurred because of the ureterovesical junction (UVJ) dysfunction, leading to high stresses on the wall. In the POM, the outflow rate was ultimately zero, and stresses on the wall were severe in the obstructed section. Comparing the results demonstrated that the peristalsis leads to even further dilation of the prestenosis portion. It was also observed that the reflux occurs in the ureter with VUR when the bladder pressure is high. Additionally, the urine velocity during the peristalsis was higher than the non-peristaltic ureter.