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Objectives: The main purpose of the present study was to determine the efficacy of real-time elastography (RTE) and strain elastography (STE) in the diagnosis of different thyroid diseases. We also aimed to calculate the cut-off points for the differential diagnosis of subacute thyroiditis (SAT), Graves’ disease (GD), and Hashimoto’s thyroiditis (HT), which have a similar B-mode sonographic appearance. Patients and Methods: A total of 24 patients with GD (10.9%), 94 patients with HT (42.7%), 20 patients with SAT (9.1%), and 82 individuals with normal healthy thyroids (37.3%) were included. Grayscale ultrasound evaluation of thyroid glands was performed with standard transverse and longitudinal planes before sonoelastography. Results: The strain ratios (SRs) (mean ± standard deviation) of patients with GD, HT, and SAT, and the control group (CG) were 14.7 ± 14.8, 8.4 ± 9.6, 23.2 ± 10.8, and 1.37 ± 0.8, respectively. The cut-off points of strain elastography of the patients with GD, HT, and SAT to the CG were 2.69 (sensitivity 92%, specificity 90%, area under the curve (AUC) 0.983; 95% CI), 2.18 (sensitivity 100%, specificity 85%, AUC 0.898), and 5.54 (sensitivity 100%, specificity 100%, AUC 1.000; 95% CI), respectively. The cut-off point of the strain ratios (SR) of the total amount of patients with HT and GD to SAT was 14.79 (sensitivity 80%, specificity 85%, AUC 0.869; 95% CI). Conclusion: Statistically significant differences were noted in the SR values and elasticity scores of the three experimental groups, and the CG. The elasticity scores of the SAT and HT groups were not significantly different from those of the GD group. The diagnostic performance of strain ratio elastography (P < 0.0001) was higher than that of real time elastography (P < 0.001). In terms of differentiating diagnosis, ES could differentiate SAT from HT, but it had no value in differentiating GD from HT and SAT. We also found statistically significant SRs for the differential diagnosis of SAT from GD and HT. Strain elastography could be a useful method for the differential diagnosis of SAT from a healthy population or from other types of thyroiditis such as GD and HT.