The surgical treatment for Chiari I malformation and basilar invagination has been discussed with great controversy in recent years. This paper presents a treatment algorithm for these disorders based on radiological features, intraoperative findings, and analyses of long-term outcomes. Eight-five operations for 82 patients (mean ± SD age 40 ± 18 years; range 9-75 years) with basilar invagination were evaluated, with a mean follow-up of 57 ± 55 months. Apart from the radiological features and intraoperative findings, findings on neurological examinations before and after surgery were analyzed. Long-term outcomes were evaluated with Kaplan-Meier statistics. All 77 patients with a Chiari I malformation underwent foramen magnum decompression with arachnoid dissection and duraplasty. Patients with ventral compression by the odontoid peg were managed with posterior realignment and C1-2 fusion. Patients without ventral compression did not undergo C1-2 fusion unless radiological or clinical signs of instability were detected. Thirty-three patients without ventral compression or instability underwent foramen magnum decompression without additional fusion, whereas 52 operations on 49 patients involved posterior fusion at C0-2 or C1-2 after realignment of ventral compression and/or treatment of C1-2 instability. Postoperatively, gait ataxia, swallowing functions, and suboccipital pain improved significantly in both treatment groups. In total, 79% and 73% of patients reported that their condition improved after foramen magnum decompression alone and after fusion with or without foramen magnum decompression, respectively. Progression-free survival rates at 10 years were 83% and 81%, respectively. Among the patients with basilar invagination, a subgroup consisting of 40.2% of the included patients underwent successful long-term treatment with foramen magnum decompression alone and without additional fusion. This subgroup was characterized by the absence of a ventral compression and no atlantoaxial dislocation or other signs of craniocervical instability. The remainder of patients underwent C1-2 fusion with posterior realignment of ventral compression if required. In the presence of basilar invagination, Chiari I malformation should be treated with foramen magnum decompression and duraplasty.