Alagille syndrome is a rare autosomal dominant disorder with variable expression. Liver damage, especially cholestatic, is the most common feature of the syndrome. Transgender patients may suffer from a great distress due to the discrepancy between assigned sex at birth and unaffirmed gender identity. Gender affirmation treatment options for these patients include hormone therapy (HT) to induce secondary sexual characteristics and various surgical procedures. Estrogen-based hormonal treatments have been linked to an increased risk of liver enzyme elevation and disruption of bilirubin metabolism, especially in those with a genetic susceptibility. The case presented here is the first described Alagille syndrome transgender patient to undergo gender affirmation treatment, including (HT) and vulvo-vaginoplasty surgery.