The aim of this study was to describe the well-being and mental health of Spanish adolescents by gender identity using a nationally representative sample. The sample comprised 1212 15-18-year-old adolescents who participated in the 2018 Spanish edition of the international study. Of the total sample, 90 were identified as binary transgender adolescents, 213 as nonbinary transgender adolescents, and 909 as cisgender adolescents (selected through a matching process from an original sample of 17,375 cisgender adolescents). Comparisons of frequencies and means (chi-square, -test, and analysis of variance) were used to analyze self-reported health, life satisfaction, health-related quality of life (HRQOL), psychosomatic complaints, and sense of coherence (SOC). Nonbinary transgender adolescents reported the lowest levels of perceived excellent health ( < 0.001), the highest frequency of psychological complaints ( < 0.001) and physical complaints ( < 0.05), and a lower SOC ( < 0.05) compared with both cisgender and binary transgender adolescents. Likewise, nonbinary transgender adolescents reported lower levels of life satisfaction ( < 0.001) and HRQOL ( < 0.001) than cisgender adolescents. The differences found between binary and nonbinary transgender youth highlight the diversity within the transgender community. Both research and intervention programs should consider the unique experiences within the transgender community to adapt sensitively to their needs.