Urinary tract tuberculosis (TB) is a rare extrapulmonary manifestation of TB in children. The disease is potentially underdiagnosed because it clinically resembles other urinary tract infections. A 13-year-old adolescent girl presented with pain, difficulty in micturition, and gross hematuria for almost two years before admission, and she had left flank pain since one year ago and significant loss of body weight during the illness. The close TB contact was her grandmother who was on TB treatment. Acid-fast bacilli yielded positive result, Mantoux test was positive (17 mm), urine GeneXpert MTB/Rif was positive; tuberculoma was identified on kidney histopathology, and a diuretic renogram revealed an uncorrected glomerular filtration rate (GFR) of the right and left kidney to be 32.5 mL/min/1.73 m2 and 5 mL/min/1.73 m2, respectively. During the treatment, oral anti-TB drug-induced hepatotoxicity (ADIH) occurred to the patient. This problem was solved with management according to the British Thoracic Society (BTS) guidelines. Screening TB in children is very important for a better outcome. If children complain of some complicated urinary tract infection, TB should be suspected. Optimaly treating children with urinary tract TB exagerrated with ADIH and CKD is very challenging.