We report a very rare case of atlantoaxial subluxation (AAS) with persistent first intersegmental artery (PFIA) and assimilation in the atlas (C1) vertebra. This case demonstrates the difficulty of deciding on a surgical strategy for complex anomalies. A 63-year-old man presented with gait disturbance, neck pain, and severe dysesthesia in his left arm. Past history included a whiplash injury. Dynamic X-ray studies demonstrated an irreducible AAS and assimilation of C1. This subluxation was slightly deteriorated in an extended position. A three-dimensional computed tomography angiography (3DCTA) indicated that the PFIA was located on the left side. We performed a C1 posterior arch resection and C1 lateral mass-axis pedicle screw (C1LM-C2PS) fixation using the modified technique of skewering the occipital condyle and C1 lateral mass. The patient had no postoperative morbidity and his symptoms disappeared immediately after operation. Complex anomalies cause difficulty in determining surgical strategy although several surgical methods for simple craniovertebral junction anomaly have been reported. To avoid significant morbidities associated with vertebral artery injury, surgical strategies for these complex conditions are discussed. The modified technique of a C1 lateral mass screw penetrating the occipital condyle is a viable treatment option.