The increasing incidence of papillary thyroid carcinoma (PTC) and the inadequacy of routine histologic examination in its diagnosis necessitate the application of ancillary studies like immunohistochemistry. This research aimed to investigate the scoring system and diagnosis of PTC with cytokeratin 19 (CK19), human bone marrow endothelium marker-1 (HBME-1), and galectin-3. This experimental laboratory study was performed at Babol University of Medical Sciences, Mazandaran, Iran from April 2017 to March 2019. Neoplastic and nonneoplastic tissue samples of 100 cases with a diagnosis of PTC were selected by convenience sampling. CK19, HBME-1, and galectin-3 immunohistochemistry markers were used on tissue samples. Analysis was performed using the t test and the chi-square test, as well as the receiver operator characteristic (ROC) curve (significance level P < 0.05). The CK19 staining was observed in all 100 (100%) non-neoplastic tissues, but HBME-1 and galectin-3 were positive in 36 (36%) and 14 (14%) of non-neoplastic tissues, respectively. The intensity scores of all the markers and their total had significantly different means in PTC and non-neoplastic tissues (P < 0.001). A significant difference was observed between the total score of each marker and the total score of their combination (P < 0.001). The combination of all 3 markers with an 11.5 0 cut-off for the total score showed the most sensitive (0.99) and specific (1.00) results. Interpreting CK19, HBME-1, and galectin-3 with the aid of the proposed scoring system was fruitful. HBME-1 and galectin-3 can be used individually or in combination for the diagnosis of PTC.