Abstract Background There are limited data discussing long-term pain relief and comparability of different image-guided sacroiliac joint (SIJ) injection. This study compared CT and fluoroscopic-guided SIJ injections regarding statistically and clinically significant differences in numeric pain reduction, radiation doses, and patient’s satisfaction. Methods A prospective study conducted on 52 patients who met specific inclusion criteria of SIJ pain. A mixture of 1 ml of 40 mg methylprednisolone acetate diluted in 2 ml of lidocaine 2% was injected under either CT or fluoroscopic guidance. Numeric rating score (NRS) and Oswestry disability index (ODI) were assessed and recorded for each patient before procedure and one-week, and one-, three-, six-, and 12-months after procedure. The results were compared between both groups. Results Analysis of NRS one-month post-procedure showed a significant decrease from baseline in both groups: 12.5% in CT group (p = 0.002) and 9.5% in fluoroscopic group (p = 0.006). No significant difference in NRS between two groups at one- and three-months post-procedure (p = 0.11 and 0.1, respectively). There was a significant difference in NRS between two groups at six- and 12-months post-procedure (p = 0.001 and < 0.0001, respectively). Comparison of ODI at six-month post-procedure revealed that both groups had a statistically significant improvement (p < 0.0001). There was a significant difference in ODI between two groups at six-months post-procedure (p = 0.01). Conclusions CT-guided SIJ injection compares favorably with fluoroscopic guidance and offers statistically and clinically significant long-term pain relief. The use of dose reduction protocol in CT is important for decreasing the radiation dose.