Introduction: Extrapulmonary tuberculosis (EPTB) represents a major diagnostic challenge in Morocco, accounting for 49% of tuberculosis cases. Conventional methods have limitations in sensitivity and turnaround time. This study evaluates the performance of the Xpert MTB/RIF system in diagnosing EPTB and detecting rifampicin resistance. Methods: A retrospective study was conducted on 413 samples (cerebrospinal fluid, urine, pus, biopsies) from 402 patients suspected of EPTB between January and December 2021. Compared techniques included microscopy (Ziehl-Neelsen staining), Löwenstein-Jensen culture, and the GeneXpert MTB/RIF test. The diagnostic performance of the latter was calculated against culture (gold standard). Results: Positivity rates were 9.5% for microscopy, 16.2% for GeneXpert MTB/RIF, and 11.3% for culture. GeneXpert showed a sensitivity of 82.6% and specificity of 92%. Among GeneXpert-positive cases, 41.7% were microscopy-negative, confirming its utility for paucibacillary forms. The highest detection rates were for pus (93%) and osteoarticular samples (100%), while cerebrospinal fluid had the lowest (60%). Rifampicin resistance detected by GeneXpert MTB/RIF was 2.98%. Conclusion: GeneXpert MTB/RIF significantly improves the diagnosis of EPTB, particularly for microscopy-negative samples. While a negative result does not rule out the diagnosis, its use as a first-line test enables more timely clinical management. Additional studies are needed to evaluate its performance in low-endemic settings.