Patellofemoral (PF) maltracking is a critical factor predisposing to PF pain syndrome. Many novel techniques of measuring patellar tracking remain research tools. This study aimed to develop a method to measure the in vivo patellar tracking and finite helical axis (FHA) by using a static magnetic resonance (MR) based methodology. The geometrical models of PF joint at 0°, 45°, 60°, 90°, and 120° of knee flexion were developed from MR images. The approximate patellar tracking was derived from the discrete PF models with a spline interpolation algorithm. The patellar tracking was validated with the previous in vitro and in vivo experiments. The patellar FHA throughout knee flexion was calculated. In the present case, the FHA drew an “L-shaped” curve in the sagittal section. This methodology could advance the examination of PF kinematics in clinics, and may also provide preliminary knowledge on patellar FHA study.