Gender diverse individuals who do not conform to society’s binary gender expectations are more likely to experience difficulties in acceptance and in recognition of gender, compared to binary-identifying transgender people. This may accentuate the feeling that their gender identity is not socially recognized or validated. This study aimed to investigate psychological functioning among gender diverse adolescents and adults who identify beyond the binary gender spectrum. In both study populations, 589 clinically-referred gender diverse adolescents from the UK (n = 438 birth-assigned females and n = 151 birth-assigned males), and 632 clinically-referred gender diverse adults from the Netherlands (n = 278 birth-assigned females and n = 354birth-assigned males), we found that a higher degree of psychological problems was predicted by identifying more strongly with a non-binary identity. For adolescents, more psychological problems were related to having a non-binary gender identity and being assigned female at birth. In the adult population, experiencing psychological difficulties was also significantly related to having a stronger non-binary identity and having a younger age. Clinicians working with gender diverse people should be aware that applicants for physical interventions might have a broader range of gender identities than a binary transgender one, and that people with a non-binary gender identity may, for various reasons, be particularly vulnerable to psychological difficulties.