Despite the recent advent of various radiographic imaging techniques, it is still very difficult to correctly distinguish a pediatric osteolytic lesion in the occipital condyle, which makes it further complicated to decide on the necessity of and the adequate timing for radical resection and craniocervical fusions. To establish a legitimate therapeutic strategy for this deep-seated lesion, surgical biopsy is a reasonable choice for first-line intervention. The choice of surgical approach becomes very important because a sufficient amount of histological specimen must be obtained to confirm the diagnosis but, ideally, the residual bony structures and the muscular structures should be preserved so as not to increase craniocervical instability. In this report, we present our experience with a case of solitary Langerhans cell histiocytosis (LCH) involving the occipital condyle that was successfully treated with minimally invasive surgical biopsy with a far lateral condylar approach supported by preoperative 3D computer graphic simulation. An 8-year-old girl presented with neck pain. Magnetic resonance imaging and computed tomography (CT) revealed an osteolytic lesion of the left occipital condyle. At surgery, the patient was placed in the prone position. A 3-cm skin incision was made in the posterior auricular region, and the sternocleidomastoid and splenius capitis muscles were dissected in the middle of the muscle bundle along the direction of the muscle fiber. Under a navigation system, we approached the occipital condyle through the space between the longissimus capitis muscle and the posterior belly of the digastric muscle and lateral to the superior oblique muscle, verifying each muscle at each depth of the surgical field and, finally, obtained sufficient surgical specimen. After the biopsy, her craniocervical instability had not worsened, and chemotherapy was performed. Twelve weeks after chemotherapy, her neck pain had gradually disappeared along with her torticollis, and CT showed remission of the lesion and marked regeneration of the left occipital condyle. Within our knowledge, this is the first reported case of LCH involving the occipital condyle. Although very rare, our case indicated that LCH can be an alternative in the differential diagnosis of osteolytic lesions in the craniocervical junction, in which early bone regeneration with sufficient cervical stability is expected after chemotherapy. In cases of pediatric osteolytic lesions, when they initially presented with apparent cervical instability, craniocervical fusion may possibly become unnecessary after a series of treatments. Thus, the effort to maximally preserve the musculoskeletal structure should be made until its histological diagnosis is finally confirmed.