Background: The thyroid gland is responsible for various functions, but it is susceptible to pathologies. The gold standard for preliminarily diagnosing thyroid abnormalities is fine-needle aspiration cytology (FNAC), although it has some limitations; thus, postoperative histopathological examination confirms the diagnosis. The aim of the present study was to compare preoperative FNAC results with postoperative histopathological examination. Methods: This study is a retrospective study based on FNAC and postoperative histopathology examination, which were compared and analyzed. Results: This study included 344 patients between 18 and 86 years old (mean age: 53.06 ± 13.89), comprising 274 females and 70 males (mean ages 52.72 ± 13.86 and 54.39 ± 14.05, respectively) with a 3.9:1 female-to-male ratio. Statistical significance between the FNAC and histopathology results was observed (p = 0.0000), and 86 (25.00%) patients were found to have been diagnosed incorrectly based on FNAC. The sensitivity of FNAC was 92.31%, and its specificity was 82.08%, with positive and negative predictive values of 68.57% and 96.08%, respectively. Conclusions: Due to many factors, FNAC may lead to over- or under-diagnosis, increasing the chances of complications associated with the selected treatment. However, we do not have any other more accurate tools; therefore, FNAC should still remain as the gold standard of preliminary examination.