Extrapulmonary tuberculosis (EPTB) is a multifaceted disease that could potentially impact nearly all organs. Current global data indicate a significant variation in the proportion of EPTB among all tuberculosis cases, ranging from 15% to 53%. Clinicians in India express concerns about the efficacy of the cartridge-based nucleic acid amplification test (CBNAAT) in EPTB, as its yield frequently does not align with the findings of the World Health Organization meta-analysis. Hence, the present study was conducted to evaluate the diagnostic yield of CBNAAT in EPTB at a tertiary care hospital. Specifically, the present hospital-based observational cross-sectional study was conducted at the Department of Respiratory Medicine at a tertiary care hospital from February 2024 to April 2024. A total of 52 patients with presumptive EPTB were enrolled. Demographic information, clinical history, and clinical examination findings were recorded with the help of a standard, semi-structured, pre-validated case record proforma. A composite reference standard (CRS), which was defined by clinical, radiological, laboratory, and histopathological findings and treatment response to antitubercular therapy along the course, was considered. The statistical software, namely SPSS 22.0, was used for the analysis of the data. Among a total of 52 patients, the mean age of patients was 37.42±16.18 years, with the proportion of males being 59.62%. The majority of patients had tuberculosis pleural effusion (63.46%). The pooled diagnostic yield of CBNAAT showed sensitivity and specificity of CBNAAT compared to CRS of 22.22% and 100%, respectively. Culture had the highest sensitivity in diagnosing EPTB in the study population, as compared to CBNAAT, thereby emphasizing the importance of diagnosis by culture method.