This novel study pushed forth current research by evaluating the effects of a clay art therapy (CAT) program on emotion regulation and the level of hair cortisol as a physiological response. Forty-one students aged 15-17 years with at least a mild form of emotional problems were randomized into a CAT group and a waitlist control (CON) group. The CAT group comprised six 2-h weekly sessions led by an experienced art therapist. Wilcoxon t-tests, Mann-Whitney U tests and a full regression model were employed to analyze the results. The study supports the positive effect of CAT on the emotion regulation ability of youth. The elevation of HCC after intervention may not be pathological but a sign of benefit to health.