Objective: Gender incongruence (GI) is a condition in which an individual’s gender identity, role, and expression differ from their assigned sex. This study aimed to evaluate when GI first arises in transgender and non-binary individuals seeking hormone therapy and their years living untreated in South Korea. Methods: This retrospective study analyzed GI patients seeking gender-affirming hormone therapy (GAHT) or surgery between 2015 and 2021. The recorded data included gender identity, legal transition status, age of onset of GI, age at the initiation of therapy, and total therapy duration. Results: In total, 337 patients were enrolled, including 149 (44.2%) transgender men, 153 (45.4%) transgender women, and 35 (10.4%) non-binary individuals. The mean age of onset of GI was 10.6 years (standard deviation, 5.1). Of the total patients, 29% had an onset of GI before age 6 years (preschool), 61% before age 12 (elementary-school), and 87% before age 15 (middle-school). Patients lived with GI for almost 14 years before GAHT initiation at a median age of 23.0 years. 90% of transgender men, 82.3% of transgender women, and 85% of non-binary patients disclosed their gender identities to their families. Regarding social transition, 31.5% of transgender men, 16.3% of transgender women, and none of the non-binary patients (P<0.005) changed their legal gender markers. Conclusion Many transgender and non-binary individuals experience GI early in life. These findings emphasized the need for early evaluation, timely gender-affirming care, and more accessible legal processes for gender marker changes in South Korea, aiming to enhance the safety and well-being of these individuals.