Tuberculosis (TB) of the shoulder joint is a rare extrapulmonary manifestation of skeletal TB. Multidrug-resistant TB (MDR-TB) involving the shoulder joint poses diagnostic and therapeutic challenges. We report a case series of three patients with shoulder joint TB, focusing on one case of rifampicin- and fluoroquinolone-resistant TB successfully managed under the National Tuberculosis Elimination Program (NTEP) with a modified all-oral longer regimen including delamanid (DLM). The report highlights the importance of early molecular diagnostics and individualized treatment regimens in extrapulmonary MDR-TB.