A 16-year-old Japanese girl who was a high school student noticed left knee joint pain with joint motion and a decrease in weight-bearing ability, which started nine months before her initial presentation to our facility. On physical examination, joint effusion, spontaneous pain and tenderness in the medial side of the left knee were noted. The full range of motion of the left knee was preserved; there was no color change or redness of the overlying skin. Laboratory test results showed no abnormalities. Radiographs of the left knee showed a radiolucent lesion with marginal sclerosis in the distal epiphysis of the left femur. On magnetic resonance imaging (MRI) (1.5T Signa; General Electric Medical Systems, Milwaukee, WI, USA), the T1-weighted (repetition time (TR) 417ms, echo time (TE) 8ms) spin-echo image enhanced by gadolinium-diethylenetriaminepenta-acetic acid (Gd-EDTA) showed hyper-intensity and iso-intensity signals with bone edema around the lesion. Computed tomography of the left knee showed no link between the tumor cavity and joint space. A histopathological examination of a small incisional biopsy conducted before operation was suggestive of chondroblastoma. The lesion was found to be deep to the medial condyle; it spread beyond the growth plate and contacted the origin of the posterior cruciate ligament of the knee. We planned to use a navigation system for precise curettage of the lesion, in addition to endoscopy to view the lesion directly through the small fenestra of the bone. The Stealth Station® Tria® Navigation System (Medtronic Navigation, Inc, Louisville, CO, USA) was used for computer-navigation surgical treatment. This navigation system consists of a computer workstation, a reference frame with passive markers, a standard probe, and an electro-optical camera connected to the computer workstation that serves as a position sensor. Since no specific application has been developed to support the resection of tumors, we used the ‘Spine’ module developed for pedicle screw application. The system uses CT data to set the region of interest. For routine CT-based navigation, paired point-based registration uses fiduciary markers that are fixed invasively to the surface of the involved bone. In the current study, multiple skin-point markers were used to avoid such an invasive marking procedure. Knee arthroscopy was performed first to examine the posterior cruciate ligament origin; however, no apparent communication was found between the medial compartment of the knee joint and the osseous lesion. Under navigation system guidance, a small skin incision (2cm in length) was made over the medial femoral condyle. A small fenestration hole (approximately 1.5cm in diameter) was made on the femoral cortex. Using the navigation system, curettage of the lesion was performed, with confirmation of the curettage area. Additional curettage and abrasion of the lesion were undertaken using the endoscope. Histopathology results showed proliferation of oval short-spindle cells and osteoclast-like multinucleated giant cells, accompanied by blue-colored or pink-colored chondroid matrix. Focal osteoid formations were also observed. After the CT-based navigation and endoscopy for curettage of the lesion, the defect was completely filled with autograft bone and β-tricalcium phosphate granules (OSferion® Olympus, Tokyo, Japan). Our patient’s post-operative course was uneventful, and follow-up radiography showed excellent filling of the autograft and artificial bone in the medial femoral condyle. Our patient is doing well at one year after surgery.