Thanatophoric dysplasia (TD) is a severe and typically fatal skeletal disorder caused by mutations in the FGFR3 gene, often leading to perinatal death. It is characterized by extreme short-limb dwarfism and, occasionally, associated anomalies such as hydronephrosis. Prenatal diagnosis, usually made in the third trimester through ultrasound and genetic testing, is crucial for guiding management decisions. Here, we report a case of TD with hydronephrosis diagnosed at 24 weeks of gestation in a 24-year-old primigravida from rural southern India. Ultrasound findings included significantly short and curved long bones, leading to the termination of the pregnancy. A post-termination examination confirmed the presence of dysplastic bones, a large head, and hydronephrosis, with histopathological analysis revealing obstructive uropathy. This case underscores the rarity of TD with hydronephrosis and highlights the importance of early and accurate prenatal diagnosis through ultrasound and molecular testing. Despite the challenges in diagnosing TD, especially when additional anomalies are present, early detection in the second trimester can play a crucial role in guiding genetic counseling and management decisions.