Tuberculosis, caused by Mycobacterium tuberculosis, is a persistent and significant health challenge that continues to affect people worldwide. Genitourinary tuberculosis is considered the second most common type of extrapulmonary tuberculosis after tubercular lymphadenitis. However, it is frequently missed due to its insidious onset and nonspecific symptoms, leading to complications like ureteric stricture, pyelonephritis, and pyonephrosis followed by nonfunctioning kidney and end-stage renal disease. Here, we report the case of a 37-year-old male who presented to the outpatient department with complaints of pain and burning micturition, accompanied by intermittent fever persisting for 1 week. A comprehensive diagnostic evaluation revealed hydronephrosis with significantly reduced cortical function of the left kidney (5.38%), an evolving abscess, and ureteric strictures. Due to multiple negative cultures for bacteriuria and persistent symptoms, the urine was also tested using cartridge-based nucleic acid amplification test (CBNAAT) to detect M. tuberculosis, which turned out to be positive. Consequently, the patient was scheduled for a planned nephrectomy after 4-month course of antitubercular treatment (ATT) with rifampin, isoniazid, pyrazinamide, and ethambutol. Nephrectomy confirmed tubercular pyonephrosis on the basis of histopathological findings of granulomatous lesions with caseous necrosis and a positive stain for acid-fast bacilli (AFB). Thus, adequate knowledge and awareness of tuberculosis combined with early detection can prevent severe complications, resulting in nephrectomy.