Purpose To evaluate the differences in MR findings between nonhemophilic hemosiderotic synovitis (HS) and diffuse-type tenosynovial giant cell tumor (D-TGCT) of the knee. Methods This study included 13 patients with histopathologically confirmed intra-articular hemosiderin deposition of the knee (eight with nonhemophilic HS and five with D-TGCT) who underwent preoperative MR imaging including T2*weighted images (T2*WI). We retrospectively reviewed the MR images and compared MR findings between the two pathologies. Results Lateral meniscus tear and lateral articular cartilage injury (88% vs. 20%, p < 0.05) and distribution in the suprapatellar bursa of the maximum thickness of T2* hypointense synovium (75% vs. 0%, p < 0.05) were significantly more frequent in nonhemophilic HS than in D-TGCT, respectively. Among patients who underwent contrast-enhanced imaging, all five patients with nonhemophilic HS showed minimal to mild enhancement of the thickened synovium with superficial linear enhancement, whereas all four patients with D-TGCT showed moderate to severe enhancement (p < 0.01). Conclusion As compared with D-TGCT, lateral meniscus tear, lateral articular cartilage injury, lesser degree of contrast enhancement of the thickened synovium, and distribution in the suprapatellar bursa of the maximum thickness of T2* hypointense synovium were characteristic features of nonhemophilic HS.