Obstruction in the ureter flow path is one of the most common problems in urinary-related diseases. As the ureter transports the urine using the expansion bolus created by the peristaltic pulses, an obstruction in its path can cause unwanted backflow and can also result in damage to the wall. But in order to understand this further, and specifically to quantify and parametrize the effect of the obstruction in the ureter, a detailed study investigating various level of obstructions in peristaltic ureter flow is necessary. In the current study, full 3D numerical simulations of peristalsis in an obstructed ureter are carried out using a finite element solver along with a two-way coupling between the fluid and structural domain with the arbitrary Eulerian-Lagrangian method. Analysis of the results shows that the larger the obstruction, the higher the wall shear stress and pressure gradient in the fluid. In addition, the amount of backflow increases with increase in the obstruction.