Congenital tuberculosis (TB) is a rare disease with a high mortality rate, and is difficult to diagnose. Here we present a case of congenital TB detected by the T-SPOT.TB assay in a male infant after in vitro fertilization. He ultimately survived after anti-TB therapy despite a delayed diagnosis, and underwent radiological follow-up. The delay in diagnosis of congenital TB resulted in a severe lung lesion, as evidenced by prolonged oxygen dependence, predisposing to recurrent pneumonia. Radiological follow-up revealed uniform rim calcification of multiple enlarged lymph nodes in the mediastinum, and long-term consolidation in the bilateral lung, with slow radiographic regression of the lung lesion. To the best of our knowledge, this is the first report on using the T-SPOT.TB assay in the detection of congenital TB, and no case of congenital TB with such clinical features and image findings has been described in previous reports.