To evaluate patients’ radiation exposure undergoing CT-guided joint injection in preparation of MR-arthrography. We developed a novel ultra-low-dose protocol utilizing tin-filtration, performed it in 60 patients and compared the radiation exposure (DLP) and success rate to conventional protocol (26 cases) and low-dose protocol (37 cases). We evaluated 123 patients’ radiation exposure undergoing CT-guided joint injection from 16 January–21 March. A total of 55 patients received CT-guided joint injections with various other examination protocols and were excluded from further investigation. In total, 56 patients received shoulder injection and 67 received hip injection with consecutive MR arthrography. The ultra-low-dose protocol was performed in 60 patients, the low-dose protocol in 37 patients and the conventional protocol in 26 patients. We compared the dose of the interventional scans for each protocol (DLP) and then evaluated success rate with MR-arthrography images as gold standard of intraarticular or extracapsular contrast injection. There were significant differences when comparing the DLP of the ultra-low-dose protocol (DLP 1.1 ± 0.39; p < 0.01) to the low dose protocol (DLP 5.3 ± 3.24; p < 0.01) as well as against the conventional protocol (DLP 22.9 ± 8.66; p < 0.01). The ultra-low-dose protocol exposed the patients to an average effective dose of 0.016 millisievert and resulted in a successful joint injection in all 60 patients. The low dose protocol as well as the conventional protocol were also successful in all patients. The presented ultra-low-dose CT-guided joint injection protocol for the preparation of MR-arthrography demonstrated to reduce patients’ radiation dose in a way that it was less than the equivalent of the natural radiation exposure in Germany over 3 days—and thereby, negligible to the patient.