Skull base ENT (Ear, Nose, and Throat) pathologies present a diagnostic challenge due to their intricate location. Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) scans are commonly used diagnostic tools for detecting these pathologies. This study aims to associate the diagnostic exactness of MRI and CT scans in detecting skull base ENT pathologies. Aim: The primary objective of our current research is to assess and associate the diagnostic accuracy of MRI and CT scans in detecting skull base ENT pathologies, including tumors, infections, and congenital anomalies. Methods: Researchers led the retrospective study of medical records from the cohort of patients with suspected skull base ENT pathologies who underwent both MRI and CT scans. Imaging reports were reviewed by experienced radiologists blinded to the clinical outcomes. Diagnostic accuracy metrics, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were calculated for each modality. McNemar's test was utilized to assess statistical significance of differences in diagnostic accuracy between MRI and CT. Results: An overall of 150 individuals were involved in our research. MRI demonstrated a sensitivity of 87%, specificity of 92%, PPV of 85%, and NPV of 93% in detecting skull base ENT pathologies. CT scans showed a sensitivity of 72%, specificity of 78%, PPV of 70%, and NPV of 80%. The diagnostic accuracy of MRI was significantly higher than that of CT for detecting these pathologies (p < 0.05). Subgroup analyses were performed for different types of pathologies, providing valuable insights into the strengths and limitations of each imaging modality. Conclusion: This comparative analysis highlights the superior diagnostic accuracy of MRI over CT scans in detecting skull base ENT pathologies. MRI offers higher sensitivity and specificity, making it a valuable tool for clinicians in the evaluation and management of individuals with these conditions. However, CT may still have a role in specific cases where MRI is contraindicated or for initial screening. Clinicians should consider these findings when selecting the most appropriate imaging modality for patients with suspected skull base ENT pathologies.