Background Self-harm in children and adolescents is difficult to treat. Peripheral and neural correlates of self-harm could lead to biomarkers to guide precision care. We therefore conducted a scoping review of research on peripheral and neural correlates of self-harm in this age group. Methods PubMed and Embase databases were searched from January 1980-May 2020, seeking English language peer-reviewed studies about peripheral and neural correlates of self-harm, defined as completed suicide, suicide attempts, suicidal ideation, or non-suicidal self-injury (NSSI) in subjects, birth to 19 years of age. Studies were excluded if only investigating self-harm in persons with intellectual or developmental disability syndromes. A blinded multi-stage assessment process by pairs of co-authors selected final studies for review. Risk of bias estimates were done on final studies. Results We screened 5537 unduplicated abstracts, leading to the identification of 79 eligible studies in 76 papers. Of these, 48 investigated peripheral correlates and 31 examined neural correlates. Suicidality was the focus in 2/3 of the studies, with NSSI and any type of self-harm (subjects recruited with suicidality, NSSI, or both) investigated in the remaining studies. All studies used observational designs (primarily case-control), most used convenience samples of adolescent patients which were predominately female and half of which were recruited based on a disorder. Over a quarter of the specific correlates were investigated with only one study. Inter-study agreement on findings from specific correlates with more than one study was often low. Estimates of Good for risk of bias were assigned to 37% of the studies and the majority were rated as Fair. Conclusions Research on peripheral and neural correlates of self-harm is not sufficiently mature to identify potential biomarkers. Conflicting findings were reported for many of the correlates studied. Methodological problems may have produced biased findings and results are mainly generalizable to patients and girls. We provide recommendations to improve future peripheral and neural correlate research in children and adolescents, ages 3-19 years, with self-harm.