Extra-pulmonary tuberculosis (EPTB) can affect any organ of the body, producing a wide variety of clinical manifestations that make the diagnosis and treatment of EPTB challenging. The optimum treatment varies depending on the site of EPTB, its severity, and response to treatment. There is often uncertainty about the best management practices, with a significant departure from national guidelines. This study aims to identify gaps and barriers in adhering to the national guidelines for the diagnosis and treatment of EPTB. We included 433 patients having EPTB and followed up at predefined intervals of 2 months, 6 months, 9 months, and 12 months. Questionnaire-based interviews of the treating physician and the patients in different departments were conducted. For confirmatory diagnosis, heavy dependence on clinical-radiological diagnosis without microbiological support was observed, which is a deviation from National Tuberculosis Elimination Programme (NTEP) guidelines and raises concerns about the potential for misdiagnosis and overtreatment. Apart from patient delays, long health system delays in EPTB were observed. The median patient delay, health system delay, and total treatment delay times were 4.2, 4, and 10.1 weeks, respectively. To enhance EPTB diagnosis and management, there is a pressing need for improved access to microbiological testing, enhanced physician training on adherence to NTEP guidelines, and greater utilisation of imaging and histopathological techniques.