Müllerian anomalies significantly impact female reproductive health. This study aims to compare the diagnostic efficacy of three-dimensional ultrasound (3D-US) and magnetic resonance imaging (MRI) in detecting and classifying these anomalies. A retrospective analysis of 150 patients with Müllerian anomalies was conducted at Saveetha Medical College and Hospital from March 2018 to March 2024. MRI and 3D-US examinations were performed and analyzed independently by two radiologists. Anomalies were classified according to European Society of Human Reproduction and Embryology (ESHRE)/European Society for Gynaecological Endoscopy (ESGE) and American Society for Reproductive Medicine (ASRM) guidelines. The septate uterus was the most prevalent anomaly, observed in 53 patients (35.3%). MRI demonstrated superior diagnostic accuracy (AUC 0.92) compared to 3D-US (AUC 0.88). Significant associations were found between presenting symptoms and specific anomaly types (p < 0.05). Inter-rater reliability between the two radiologists, with respect to classification of anomalies, was high (Cohen's kappa 0.85). MRI's superior soft-tissue contrast and multiplanar capabilities make it the gold standard for evaluating complex uterine malformations. 3D-US offers valuable real-time imaging and is particularly effective in assessing septum characteristics. The combined use of MRI and 3D-US enhances diagnostic precision and facilitates tailored management strategies. Integrating MRI and 3D-US in clinical practice improves diagnostic accuracy and treatment planning for Müllerian anomalies, ultimately enhancing patient outcomes.