Tuberculous infection of the tracheobronchial tree, termed as endobronchial tuberculosis (EBTB), is more common in young adults and females. This clinical entity is poorly understood and the diagnosis is frequently delayed as sputum smears are often negative for acid fast bacilli and the chest radiograph can be normal, resulting in diagnostic confusion. Bronchoscopy continues to play a key role in its diagnosis. Though atelectasis is not uncommon in these patients, EBTB presenting as a middle lobe syndrome (MLS) has rarely been documented. MLS refers to chronic or recurrent collapse of the right middle lobe and has a myriad of causes. The pathogenesis of this entity too is not fully established. We report this exceptional clinical manifestation in a 19-year-old male, who presented for evaluation of respiratory symptoms for 6 months along with constitutional complaints. Imaging suggested the presence of MLS and bronchoscopy established the diagnosis of endobronchial tuberculosis. GeneXpert evaluation of bronchial aspirate detected Mycobacterium tuberculosis. Histopathology confirmed the presence of granulomatous lesions. Subsequently, the cultures of bronchial aspirate and post-bronchoscopy sputum grew M. tuberculosis. Appropriate therapy with anti-tuberculosis drugs resulted in a remarkable symptomatic and radiological improvement. EBTB presenting as a MLS is a distinct rarity.