<p>An increasing heterogeneity of clinical presentations and varying levels of psychological problems characterize gender dysphoria (GD) in adolescents. These clinical patterns suggest distinct developmental trajectories. Here, we examine the onset age of GD, i.e., the percentage of early onset (EO) vs. late onset (LO), and its association with internalizing problems in adolescents with GD. The sample consisted of 462 adolescents (11–18 years, <i>M</i>_age = 15.46 years; 392 birth-assigned females, 70 birth-assigned males) who attended the Hamburg Gender Identity Service for Children and Adolescents (Hamburg GIS) in Germany between 2013 and 2021. Onset age was self-reported during clinical interviews and then later scored by clinicians using a DSM-5 rating sheet. When adolescents retrospectively met criteria A and B for childhood-onset GD, they were rated as having an EO. Those who fulfilled neither criteria A nor B in childhood were considered to have a LO. Internalizing problems were assessed using the Youth Self-Report. Overall, 51% (<i>n</i> = 237) of adolescents with GD presented with an EO and 49% (<i>n</i> = 225) reported diagnostic criteria related to a LO. More than half of the sample (58%, <i>n</i> = 266) fell within the clinical range for internalizing problems. Furthermore, LO (as opposed to EO) was significantly associated with reporting more internalizing problems. Our findings emphasize that adolescents with LO represent a particularly vulnerable group whose needs should be considered more closely diagnostically and treatment-wise. A protocol-based approach to the indication of physical interventions may not adequately address current clinical presentations and should be complemented by a differential approach based on individual adolescent development.</p>