We report the case of a 12-year-old boy with flexion loss in the left elbow caused by deficient of the concavity corresponding to the coronoid fossa in the distal humerus. The range of motion (ROM) was 15°/100°, and pain was induced by passive terminal flexion. Plain radiographs revealed complete epiphyseal closure, and computed tomography (CT) revealed a flat anterior surface of the distal humerus; the coronoid fossa was absent. Then, the bony morphometric contour was surgically recreated using a navigation system and a three-dimensional elbow joint model. A three-dimensional model of the elbow joint was made preoperatively and the model comprising the distal humerus was milled so that elbow flexion flexion of more than 140° could be achieved against the proximal ulna and radius. Navigation-assisted surgery (contouring arthroplasty) was performed using CT data from this milled three-dimensional model. Subsequently, an intraoperative passive elbow flexion of 135° was obtained. However, active elbow flexion was still inadequate one year after operation, and a triceps lengthening procedure was performed. At the final follow-up one year after triceps lengthening, a considerable improvement in flexion was observed with a ROM of −12°/125°. Plain radiographs revealed no signs of degenerative change, and CT revealed the formation of the radial and coronoid fossae on the anterior surface of the distal humerus. Navigation-assisted surgery for deformity of the distal humerus based on a contoured three-dimensional model is extremely effective as it facilitates evaluation of the bony morphometry of the distal humerus. It is particularly useful as an indicator for milling the actual bone when a model of the mirror image of the unaffected side cannot be applied to the affected side as observed in our case.