The purpose of the study was to explore the diagnostic performance of acoustic radiation force impulse (ARFI) elastography in differential diagnosis between benign and malignant thyroid nodules in patients with coexistent Hashimoto’s thyroiditis (HT). A total of 141 pathological proven nodules in 141 HT patients (7 males and 134 females, mean age 50.1 years, range 23–75 years) received conventional ultrasound (US), elasticity imaging (EI) and ARFI elastography, including virtual touch tissue imaging (VTI) and virtual touch tissue quantification (VTQ), before surgery. Shear wave velocity (SWV) and SWV ratio were measured for each nodule on VTQ. The US, EI and ARFI elastography features were compared between benign and malignant nodules in HT patients. Receiver operating characteristic curve (ROC) analyses and area under curve (AUC) were performed to assess the diagnostic performance. Pathologically, 70 nodules were benign and 71 nodules were malignant. Significant differences were found between benign and malignant nodules in HT patients for EI (EI score) and ARFI (VTI grade and SWV) (all P value <0.05). The AUCs for EI, VTI, SWV and SWV ratio were 0.68 [95 % confidence interval (CI): 0.59–0.77], 0.90 (95 % CI: 0.84–0.95), 0.77 (95 %CI: 0.70–0.85) and 0.74 (95 %CI: 0.66–0.82), respectively. The cut-off points were EI score ≥3, VTI grade ≥4, SWV ≥2.58 m/s and SWV ratio ≥1.03, respectively. In conclusion, ARFI elastography is useful for differentiation between benign and malignant thyroid nodules in HT patients. The diagnostic performance of ARFI elastography is better than EI.