The gelatin-thrombin matrix, Floseal, is an excellent novel hemostatic agent that is used in various surgical fields. Thrombin is a serine protease, and the conversion of prothrombin to thrombin is an essential step in the coagulation cascade. However, thrombin can induce blood-brain barrier (BBB) disruption and vasogenic brain edema. This report describes two cases of gelatin-thrombin matrix-related cyst formation after cerebral hematoma evacuation. An 82-year-old man with a gelatin-thrombin matrix-related cyst was treated by cyst drainage and fenestration to the lateral ventricle. Histological evaluation of the cyst wall showed a gelatin-thrombin matrix reserve, marked infiltration of inflammatory cells, and foam cell accumulation. In addition, an 85-year-old woman with a gelatin-thrombin matrix-related cyst was treated with steroids and responded well. In both cases, the post-treatment course was uneventful. Cyst shrinkage and no recurrence were observed. The gelatin-thrombin matrix can cause cyst formation with brain edema. This is the first report demonstrating the cyst wall pathology and the steroid responsivity on cyst shrinkage. The mechanism of cyst formation is thought to be thrombin-induced BBB disruption. Excess gelatin-thrombin matrix should be carefully removed from the surgical beds, particularly those having a blinded space from the neurosurgical microscope.