Purpose To evaluate the effectiveness of posterior occipitocervical reconstruction using the anchors of cervical pedicle screws and plate-rod systems for patients with congenital osseous anomalies at the craniocervical junction. Methods Twenty patients with congenital osseous lesions who underwent posterior occipitocervical fusion using the anchors of cervical pedicle screws and plate-rod systems for reduction and fixation from 1996 to 2009 were reviewed. The lesions included os odontoideum, occipitalization of the atlas, congenital C2-3 fusion, congenital atlantoaxial subluxation, congenital basilar invagination and combined anomalies. The clinical assessment and the measurements of the images were performed preoperatively, postoperatively and at most recent follow-up. Results The combined deformity of flexion of the occipitoatlantoaxial complex and invagination of the odontoid process associated with congenital osseous lesions at the craniocervical junction was corrected by application of combined forces of extension and distraction between the occiput and the cervical pedicle screws. Preoperative myelopathy improved in 94.7 % patients. The mean Ranawat value, Redlund-Johnnell value, atlantodental distance, occiput (O)-C2 angle, and C2-C7 lordosis angle improved postoperatively and was sustained at most recent follow-up. The mean cervicomedullary angle improved from 129.3°preoperatively to 153.3°postoperatively. The mean range of motion at the lower adjacent motion segment remained unchanged at most recent follow-up. The fusion rate was 95 %. Conclusions The results of the present study indicate that posterior occipitocervical reconstruction using the anchors of cervical pedicle screws and plate-rod systems is an effective technique for treatment of deformities and/or instability caused by congenital osseous anomalies at the craniocervical junction.