A computer-assisted navigation system to be used for total knee arthroplasties (TKAs) was reported to improve the accuracy of bone resection and result in precise implant placement, but the concomitant surgical invasion and time consumption are clinical problems. We developed a computed tomography (CT)-based navigation system (NNS) to be used for minimally invasive TKA. It requires only the reference points from a small limited area of the medial femoral condyle and proximal tibia through a skin incision to obtain optical images. Here we evaluated the usefulness and accuracy of the NNS in comparison with the commercially available BrainLAB image-free navigation system (BLS). In a clinical experiment, the registration times obtained with the NNS tended to be shorter than those obtained with the BLS, but not significantly so. The NNS group tended to be in the extended position in the sagittal plane of the distal femur within 3 degrees, and the BLS group showed rather flexed deviation in the sagittal plane of the anterior femur.