Abstract Purpose Intrathecal injection of nusinersen is an approved treatment of spinal muscular atrophy (SMA). CT-guided injection is a method of nusinersen administration in patients with severe scoliosis, in whom standard lumbar puncture is not feasible. The injections are repeated every 4 months for life, and accumulated radiation doses absorbed by the patient can increase the risk of cancer. In this study, we present the results of CT-guided intrathecal nusinersen injections with an ultra-low radiation dose protocol. Methods Eighteen patients (15 adults and three children) in whom standard lumbar puncture was not feasible due to severe scoliosis or spinal stabilization were included in this retrospective study. The first 23 injections were performed with a standard radiation dose protocol and the next 42 injections with an ultra-low-dose protocol. The radiation doses, measured as total dose length product (DLP), were acquired and compared between the protocols. Results Injections were successful in 100% of patients with both ultra-low-dose and standard protocols. The radiation dose, measured as DLP, was 111.2–1100.7 (Me = 248.1) mGy*cm for the standard protocol. For the ultra-low-dose protocol, the dose range was 5.0–54.4 (Me = 26.7) mGy*cm, which was significantly lower than with the standard protocol (p < 0.001, η² = 0.67). Conclusion Radiation doses can be significantly decreased in the CT-guided injection of nusinersen. The proposed protocol allows for effective CT-guided intrathecal nusinersen administration in patients with SMA and severe scoliosis.