Background: Although Hashimoto’s thyroiditis (HT) and Graves’ disease (GD) have overlapping symptoms, the treatment of these conditions is different, making the differential diagnosis of these disorders crucial for optimal patient outcomes. Therefore, we developed and evaluated a novel serological method for the differential diagnosis of HT and GD. Methods: We developed a highly sensitive, time-resolved fluoroimmunoassay for measuring serum concentrations of anti-phospholipase A2 receptor (PLA2R)-IgG antibody; other thyroid health indicators such as thyroid-stimulating hormone (TSH), free T3, free T4; and antibodies against thyroglobulin (TGAb), thyroperoxidase (TPOAb), and TSH receptor (TRAb). We analyzed the differences in the concentrations of these indicators among healthy controls, patients with HT, and patients with GD. Serum anti-PLA2R-IgG, TGAb, TPOAb, TRAb, and other indicator concentrations were used to differentially diagnose HT and GD. Results: In the control, GD, and HT groups, the average concentrations (±standard deviation) of anti-PLA2R-IgG were 0.49 ± 0.24 mg/L, 0.47 ± 0.11 mg/L, and 3.23 ± 1.89 mg/L, respectively, and the percentages of patients above the threshold of 1.1 mg/L were 0%, 0%, and 95% respectively. The positive results obtained in both the TPOAb and anti-PLA2R-IgG tests were good diagnostic indicators of HT, with a sensitivity of 90% and specificity of 100%. Conclusions: The serum anti-PLA2R-IgG antibody concentration was significantly elevated in the sera of HT patients compared with that in healthy controls and GD patients. Measurement of serum anti-PLA2R-IgG concentrations in conjunction with the TPOAb test provides a reliable method for the differential diagnosis of HT and GD. Funding Statement: Funding was provided by the Clinical Medical Science fund of Jiangsu Province (No. BL2014022), the Directive Planning Project of Wuxi Science and Technology Bureau(No. CSE31N1302), the Key Subject of Wuxi’s Hospital Administration Center (No. YGZXM14013), Wuxi Key Medical Talents (zdrc006), Jiangsu Province Science and Education Project (CXTDB2017016), Wuxi Technology Development Fund (Medical and public health project) (WX18IIAN027) and Medical and Public Health Project of Wuxi Sci-Tech Development Fund (WX18IIAN647). Declaration of Interests: The authors declare they have no competing financial interests. Ethics Approval Statement: The institutional review board of Jiangyuan Hospital and Wuxi People’s Hospital approved the study, and written informed consent was obtained from all the study subjects. Patients treated at Jiangyuan Hospital (China) and Wuxi People’s Hospital (China) between January 2015 and May 2017 were selected as the subjects for this study.