Introduction: Fine-needle aspiration cytology (FNAC) is a simple, minimally invasive, and effective tool that can be used to accurately diagnose benign and malignant lesions of the breast. The International Academy of Cytologists Yokohama system and Modified Masood’s Scoring Index (MMSI) are two important systems to categorize palpable breast lesions on FNAC. The goal of the present study was to evaluate the IAC Yokohama system and MMSI in the cytological diagnosis and classification of diverse breast lesions and to compare the diagnostic accuracy of both systems through cyto-histological correlation. Methods: A retrospective cross-sectional study was done within the 3-year period from 2019 to 2021. Seven hundred and ninety cases of FNAC breast lesions were included and were categorized following the recommendations by the International Academy of Cytologists Yokohama system and MMSI. The sensitivity, specificity, accuracy, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy for both systems were calculated, taking histopathology as the standard. Additionally, the risk of malignancy (ROM) of each category was calculated in the Yokohama system. Results: The IAC Yokohama system’s sensitivity, specificity, PPV, NPV, and diagnostic accuracy were 96.8, 95.8%, 96%, 96.6%, and 96.3%. The MMSI had sensitivity, specificity, PPV, NPV, and diagnostic accuracy of 95.8%, 98.4%, 98.3%, 96.1%, and 97.1%, respectively. The ROM for insufficient, benign, atypical, suspicious for malignancy, and malignant categories were 12.5%, 1.8%, 20%, 90.4%, and 97.5%, respectively. Conclusion: The categorization of breast lumps using the MMSI is more accurate and more specific in diagnosing malignant cases, and thus, the MMSI system is more precise and accurate at diagnosing malignant cases.