Background: Children and adolescents with mental health problems are widely reported to have problems with peer relationships; however, few studies have explored the way in which these children are regarded by their peers. For example, little is known about the nature of peer stigmatisation, and no published research has investigated implicit attitudes thus ensuring that stigma is not well understood. To address this issue, the current study explored patterns of explicit and implicit stigmatisation of peers with depression and attention deficit hyperactivity disorder (ADHD). Methods: The sample was 385 children (M = 10.21 years) and adolescents (M = 15.36 years). Participants completed a questionnaire assessing explicit stigma towards an age- and gender-matched peer with ADHD or depression and another peer with normal issues who were described in vignettes. They also completed a modified version of the Implicit Association Test (IAT) that explored implicit attitudes towards the target peers. Results: Questionnaire data indicated that the peer with ADHD was perceived more negatively than the peer with depression on all dimensions of stigma, except perceived dangerousness and fear. In contrast, the IAT findings suggest that some participants had more negative views of the peer with depression than the peer with ADHD. Specifically, the findings demonstrate that adolescent males demonstrated significantly stronger negative implicit evaluations of depression compared with younger males and adolescent females. Conclusions: Children and adolescents demonstrate stigmatising responses to peers with common mental health problems. The nature and extent of these responses depends on the type of problem and the type of measurement used. The findings highlight the importance of using both explicit and implicit measures of stigma.