Background: Fine needle aspiration cytology (FNAC) is widely used as a minimally invasive diagnostic technique for evaluating lesions across multiple organ systems. Histopathology remains the gold standard for definitive diagnosis. Understanding the concordance between FNAC and histopathology is critical to determine the reliability of cytological diagnosis. Objective: To evaluate the concordance between FNAC and histopathological diagnosis across various organ systems and estimate pooled diagnostic accuracy through systematic review and meta-analysis. Methods: A systematic search of PubMed, Scopus, Web of Science, and Google Scholar was conducted for studies published between 2000 and 2025 assessing FNAC–histopathology correlation. Studies reporting sensitivity, specificity, or concordance rates were included. Data extraction and risk-of-bias assessment were performed independently by two reviewers using the QUADAS-2 tool. Pooled sensitivity, specificity, and diagnostic odds ratio were estimated using a random-effects model. Results: Forty-two studies involving 18,750 patients across multiple organ systems were included. The pooled sensitivity of FNAC was 0.91 (95% CI: 0.88–0.94) and pooled specificity was 0.96 (95% CI: 0.94–0.98). The overall concordance rate between FNAC and histopathology was 92.3%. Highest concordance was observed in thyroid and breast lesions. Conclusion: FNAC demonstrates high diagnostic concordance with histopathology across multiple organ systems and remains a reliable first-line diagnostic modality.