Femoral artery bypass surgery needs postoperative monitoring due to the high complication risks after bypass. Numerical simulation is an effective tool to help solve this task. This work presents the experience of patient-specific CFD simulation of blood flow in proximal anastomosis for femoral-popliteal bypass, including patient follow-up after bypass surgery. Six cases of proximal anastomosis of femoral-popliteal bypass 3–30 months after surgery were studied. A repeated study was performed for four patients to monitor geometric and hemodynamic changes. The blood flow structure variety in proximal anastomoses and the blood flow dynamics during the cardiac cycle are described in detail using CFD simulation. Special attention is paid to time-average wall shear stresses (TAWSS) and oscillatory shear index (OSI) distributions. Low and oscillatory wall shear stresses were registered in the graft downstream from the suture, especially in case of low inlet flow. It was shown that the postoperative geometry changes led to significant hemodynamic changes; thereby, neointima has grown in areas with initially low and oscillatory wall shear stresses.