Gender dysphoria (GD) is associated with clinically significant distress and impairment in social, scholastic, and other important areas of functioning, especially when early onset is reported. The aim of the present study is to assess the psychopathological features associated with GD in adolescence, comparing a group of gender dysphoric adolescents (GDs) with a group of non-referred adolescents (NRs), in terms of body uneasiness, suicide risk, psychological functioning, and intensity of GD. A sample of 46 adolescents with GD and 46 age-matched NRs was evaluated (mean ± SD age = 16.00 ± 1.49 and 16.59 ± 1.11 respectively, p > 0.05). Subjects were asked to complete the Body Uneasiness Test (BUT) to explore body uneasiness, the Youth Self Report (YSR) to measure psychological functioning, the Multi-Attitude Suicide Tendency Scale (MAST) for suicide risk, and the Gender Identity/Gender Dysphoria Questionnaire for Adolescents and Adults (GIDYQ-AA) for GD assessment. Adolescents with GD reported significantly higher levels of body uneasiness (BUT-GSI, F = 380.13, p < 0.0001), as well as a worse psychological functioning (YSR, F = 13.06 and p < 0.0001 for "total problem scale" and F = 12.53, p = 0.001 for "internalizing" scale) as compared to NRs. When YSR subscales were considered, GDs showed significantly higher scores in the "withdrawal/depression", "anxiety/depression", and "social problems" (all p < 0.0001). In addition, GDs showed significantly higher levels in the "attraction to death" and "repulsion by life" scales and lower scores in the "attraction to life" scale (all p < 0.0001). Finally, GIDYQ-AA score was significantly lower (meaning a higher level of gender dysphoria symptoms) in GDs vs. NRs (p < 0.0001). GD adolescents reported significantly higher body dissatisfaction and suicidal risk compared to NRs. In addition, results confirmed a significant impairment in social psychological functioning in adolescents with GD.