Background: Although the single-stage posterior realignment craniovertebral junction (CVJ) surgery could treat most of the basilar invagination (BI) and atlantoaxial dislocation (AAD), there are still some cases with incomplete decompression of the spinal cord, which remains a technique challenging situation. Methods: Eleven patients were included with remained myelopathic symptoms after posterior correction due to incomplete decompression of the spinal cord. Transoral odontoidectomy assisted by image-guided navigation and intraoperative CT was performed. Clinical assessment and image measurements were performed preoperatively and at the most recent follow-up. Results: Eleven patients were followed up for an average of 47 months. Symptoms were alleviated in 10 of 11 patients (90.9%). One patient died of an unknown reason 1 week after the transoral approach. The clinical and radiological parameters pre- and postoperatively were reported. Conclusion: Transoral odontoidectomy as a salvage surgery is safe and effective for properly selected BI and AAD patients after inadequate indirect decompression from posterior distraction and fixation. Image-guided navigation and intraoperative CT can provide precise information and accurate localization during operation, thus enabling complete resection of the odontoid process and decompression of the spinal cord. © 2020 The Author(s).