This case report presents a 38-year-old transgender woman, assigned male at birth, who presented with severe right flank pain associated with nausea and hematuria. After previously undergoing gender-affirming surgeries, including abdominoplasty, liposuction, breast augmentation, and reconstructive vaginal surgery, the patient developed bilateral ureteral and kidney stones leading to significant hydronephrosis. Bilateral double J insertion was performed following a computed tomography (CT) Uroscan. This was followed by flexible ureteroscopy and laser fragmentation of the stone bilaterally. The patient's anatomy was remarkable for the presence of neovagina and prostate. This case highlights the unique challenges and considerations in managing genitourinary complications in transgender individuals. The literature is limited in the Middle East concerning transgender individuals, hence the need to conduct further research and compile comprehensive case reports on transgender individuals in the Middle East in order to establish a robust database and draw meaningful epidemiological conclusions.