Introduction: Prevalence of Extrapulmonary Tuberculosis (EPTB) due to Mycobacteriumtuberculosis and Non-Tuberculous Mycobacteria (NTM) are on the rise especially in a developing country like India. Smear Microscopy (SM) is commonly used for detection of mycobacteria. Due to the paucibacillary nature in the extrapulmonary specimens SM pose a problem in detection. Though molecular methods are increasingly used now-a-days but there are possibilities that these reactions may get inhibited due to the presence of inhibitors in the extrapulmonary specimens. Aim: To compare Mycobacterium Growth Indicator Tubes (MGIT 960) with Lowenstein Jensen (LJ) medium for the detection of mycobacteria. Materials and Methods: The current prospective study was conducted on 1879 extrapulmonary specimens collected from a tertiary care hospital during the study period from July 2018 to March 2020. Specimens were subjected to Ziehl Neelsen (ZN) staining and Auramine Phenol (AP) staining. Culture was done in both LJ media and MGIT 960 culture. Positive mycobacterial cultures were subjected to MPT64 Immunochromatographic Test (ICT). Data were analysed using the Statistical Package for Social Sciences (SPSS®) for Windows® release 21.0 (SPSS Inc., Chicago, IL, USA). Results: A total of 129 (6.9%) and 105 (5.6%) mycobacteria was isolated by MGIT 960 and by LJ culture respectively among 1879 extrapulmonary specimens. MGIT 960 identified 118 (91.5%) as Mycobacterium tuberculosis complex and 11 (8.5%) as NTM among the total mycobacteria isolated. Out of 105 mycobacteria grown by LJ culture, 95 (90.5%) and 10 (9.5%) were identified as Mycobacterium tuberculosis and NTM, respectively. The rate of contamination associated with MGIT 960 and LJ culture was 4.6% and 4.3% respectively. The Time to Detection (TTD) was found to be significantly shorter for isolation of Mycobacterium tuberculosis by MGIT 960 culture compared to LJ culture. Conclusion: In the current study, authors compared MGIT 960 with solid LJ culture for recovery of both Mycobacterium tuberculosisComplex and NTM from extrapulmonary specimens and authors found increased recovery by MGIT 960 compared to LJ culture and also shorter duration of detection for Mycobacterium tuberculosis by MGIT 960 with comparable contamination rates.