This case presents a 3-day-old phenotypical male with penile tissue, impalpable testes in scrotum and an ultrasound suggestive of a uterine structure. This is in the setting of being prostin-dependent for transposition of the great arteries with no ventricular nor atrial septal defect. Hypothalamic-pituitary-gonadal axis bloods and, specifically, anti-müllerian hormone and inhibin B levels were normal. Magnetic resonance imaging suggested an empty right hemiscrotum with a left indirect inguinal hernia, an undescended left testis, and no evidence of a uterus. This patient underwent an arterial switch operation at 2 weeks of age, followed by an exploration of the left groin and modified bilateral orchidopexy at 8 weeks of age. Findings in the latter surgery revealed bilateral gonads in the left inguinal canal with a uterus and fallopian tubes between said gonads. Disorder of sex development gene panel testing of the patient and parents was undertaken after extensive counselling. This patient is genetically male with a 46XY karyotype. Both parents were identified as carriers of the AMHR2 missense variant. We present the likely first reported case of transverse testicular ectopia in a newborn with transposition of the great arteries, which may well highlight a possible link between the two congenital anomalies.