Aim: The study aimed to evaluate the diagnostic accuracy and clinical impact of intraoperative frozen section (IFS) analysis in gastrointestinal (GI) cancer surgeries by comparing its real-time histopathological findings with final paraffin-embedded histopathology. Additionally, the study assessed the role of IFS in guiding intraoperative decision-making and optimizing surgical outcomes. Materials and Methods: This prospective study was conducted at a tertiary care hospital, including 50 patients undergoing GI cancer surgery. Patients diagnosed with gastrointestinal malignancies requiring surgical resection and IFS analysis were enrolled. Fresh tissue specimens from tumor margins and lymph nodes were collected intraoperatively and processed using rapid freezing and hematoxylin and eosin (H&E) staining for histopathological evaluation. The IFS results were compared with the final histopathology to determine sensitivity, specificity, and predictive values. Statistical analyses were performed using SPSS version 25.0, with a significance level of p<0.05. Results: The study population comprised 60% males and 40% females, with a predominant age group of 41–60 years. Colorectal cancer (40%) was the most common malignancy, followed by gastric cancer (30%). The diagnostic accuracy of IFS was high, with a sensitivity of 96%, specificity of 64%, positive predictive value of 94%, and negative predictive value of 72%. Intraoperative frozen section influenced surgical decisions in 40% of cases, leading to margin extension (24%) and additional lymph node dissection (16%). Postoperative complications occurred in 24% of patients, with a significant correlation between surgical outcomes and complications (p=0.014). Conclusion: Intraoperative frozen section analysis is a valuable tool for real-time histopathological assessment in GI cancer surgeries, improving surgical precision and reducing residual tumor risks. Despite certain diagnostic limitations, it significantly aids intraoperative decision-making and enhances oncologic outcomes. The integration of advanced pathology techniques and digital tools may further refine its accuracy and clinical utility in gastrointestinal oncology.