Our aim is to explore differences in Hector Battifora mesothelial‐1 (HBME‐1), cytokeratin‐19 (CK19), Galectin‐3 (Gal‐3), and CD56 expression in infiltrative follicular variants of papillary carcinoma (IFVPTC) and encapsulated follicular variants of papillary carcinoma (EFVPTC) and to provide clues for distinguishing the two subtypes preoperatively. Tissue microarrays from 100 EFVPTC (45 non‐invasive follicular thyroid neoplasms with papillary‐like nuclear features (NIFTP) and 55 invasive EFVPTCs), 43 IFVPTCs, and 64 follicular neoplasms (FN) were immunostained with HBME‐1, CK19, Gal‐3, and CD56. Each case was scored 1 point for every positive result. Immunohistochemical expression was not significantly different in invasive EFVPTC and NIFTP, except for that of HBME‐1. HBME‐1, CK19, Gal‐3, and CD56 expression were significantly higher in IFVPTC than in EFVPTC. At the cutoff of 3 points, the score method had special diagnostic value for differentiating IFVPTC from EFVPTC and FN and for predicting lymph node metastasis. Scoring of immunohistochemistry results may be applied to core biopsy or cell blocks to assist ultrasonographic, cytologic and molecular tests in differentiating IFVPTC and EFVPTC preoperatively, possibly appropriately guiding EFVPTC preoperatively for limited operation or active surveillance.