Purpose: To evaluate the rate of apoptosis in orbital fibroadipose tissue in Graves’ ophthalmopathy (GO) patients and investigate its associations with disease characteristics. Methods: Orbital tissue samples were obtained during decompression surgery from 25 GO patients. Disease activity was evaluated using the Clinical Activity Score, while the clinical features of GO were evaluated using the Total Eye Score (TES). Tissue samples of 12 patients without any thyroid or autoimmune disease were studied as controls. The rate of apoptosis was evaluated with a terminal deoxyribonucleotidyl transferase-mediated dUTP-digoxigenin nick-end labeling (TUNEL) assay, and ultrastructural features of apoptosis were evaluated with electron microscopy. Results: The rate of apoptosis in orbital fibroadipose tissue was significantly higher in GO cases than in the control group (p < 0.001) and significantly correlated with TES (r: 0.545; p = 0.005). The rate of apoptosis was 7.9% ± 6.5%, and 22.0% ± 7.8% in type 1 and type 2 cases, respectively (p = 0.001). The rate of apoptosis was 21.6% ± 7.5% in eyes showing dysthyroid optic neuropathy (DON) and 6.7% ± 5.4% in eyes without DON (p = 0.005). Conclusions: The rate of apoptosis was high in the orbital fibroadipose tissue of GO cases and was related to the clinical features of the disease.