A paradoxical reaction during anti-tuberculosis (anti-TB) therapy is commonly reported in patients with human immunodeficiency virus (HIV). However, a similar reaction to anti-TB therapy can also occur in patients without HIV, especially in patients who have undergone solid organ transplantation. A 65-year-old woman who underwent kidney transplantation six months prior presented to our emergency room with progressive paraparesis. She had been diagnosed with drug-susceptible miliary TB and had undergone two weeks of treatment with anti-TB medication. Magnetic resonance imaging showed a spinal intramedullary mass and multiple intracranial nodules. The etiology of the lesions was confirmed as Mycobacterium tuberculosis. We report a paradoxical reaction of spinal intramedullary and multiple intracranial tuberculomas in a patient with miliary TB who had received appropriate treatment for more than two weeks.