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Simple Summary: Core needle biopsy (CNB) and fine needle aspiration (FNA) are the most commonly used non-surgical tissue sampling methods for breast cancer diagnosis. CNB has higher diagnostic accuracy and enables molecular subtype determination for neoadjuvant chemotherapy, and is more widely used than FNA. However, FNA is less invasive and provides faster results, and is still performed by many clinicians. This study was conducted to investigate the prognosis and application criteria of the two methods in real clinical practice. We found that patients who were diagnosed with breast cancer using FNA had significantly worse survival rates than those diagnosed using CNB. In the subgroup analysis, FNA showed worse survival rates in cases of highly suspicious lesions, nonpalpable tumors, or centrally located tumors. Our study may help in choosing the appropriate tissue sampling method for suspected breast cancer cases. (1) Background: Breast core needle biopsy (CNB) is preferred over fine needle aspiration (FNA) as it has higher sensitivity and specificity and enables immunohistochemical evaluation. However, breast FNA remains widely used because of its low cost, minimally invasive nature, and quick results. Studies analyzing the effects of each test on the prognoses of patients with breast cancer are scarce and controversial, and the criteria for test selection remain unknown. (2) Methods: This study included adult female patients who underwent breast cancer surgery at 102 general hospitals. The trend of breast biopsies over time was analyzed, and the prognoses of patients with breast cancer who underwent CNB and FNA were compared. (3) Results: This study included 73,644 patients who underwent FNA (n = 8027) and CNB (n = 65,617). A multivariate Cox regression analysis showed that patients diagnosed using FNA had significantly worse overall survival (OS) and breast-cancer-specific survival (BCSS) than those diagnosed using CNB. In the subgroup analysis, patients with breast imaging reporting and data system (BI-RADS) 5 lesions, palpable tumors, or centrally located tumors had significantly worse OS and BCSS with FNA than with CNB. (4) Conclusions: CNB should be performed preferentially instead of FNA in patients with BI-RADS 5 lesions and nonpalpable or centrally located tumors. [ABSTRACT FROM AUTHOR]