Background Young transgender or gender nonconforming (TGNC) children and adolescents or those with a gender dysphoria (GD) diagnosis show an increased risk of suicidal and nonsuicidal self-harming thoughts and behaviors (STBs). Data from German-speaking regions on this topic and studies comparing self- and parent-reported STBs have been scarce. The study aims were therefore to examine: (a) frequencies of self- and parent-reported STBs in a German clinical sample of children and adolescents with GD and (b) differences between age and gender groups, as well as between self- and parent-reports. Methods Two items from the Child Behavior Checklist (CBCL) and the Youth Self-Report (YSR) were used to assess self- and parent-reported STBs in a sample of 343 adolescents and 49 children who presented to the Hamburg Gender Identity Service (Hamburg GIS) between 2013 and 2019. Seventy-eight percent of the analysis sample was assigned female at birth (AFAB), and 22% were assigned male at birth (AMAB). Results Parents reported STBs on the CBCL for 16% and 6% of the cases in childhood and for 20% and 29% of the adolescent cases, respectively. STBs were self-reported by 38% and 45% of the adolescents who could report on the YSR. STBs were higher among adolescents than among children and in self-reports (YSR) compared to parent reports (CBCL). AFAB adolescents reported higher degrees of STBs than AMAB adolescents. Conclusions Children and adolescents with GD are a high-risk population for STBs, especially pubescent and AFAB individuals. Mental health professionals should screen early for STBs to prevent possible suicidal ideation-to-action transitions.