In response to the high rate of comorbidity among different types of emotional disorders in children, Transdiagnostic Unified Protocol of Emotional disorder in children (UP-C) was developed to address common underlying mechanisms in the development and maintenance of emotional disorders using empirically supported cognitive and behavioural strategies. Although, studies supported the effectiveness of this protocol in the treatment of wide range of emotional disorders, further studies are needed to examine its effect on transdiagnostic factors. The present study aimed to investigate the efficacy of the UP-C on negative affect, anxiety sensitivity and perceived control in children with emotional disorders. During this randomized controlled trial, 34 children aged 7 to 13 with emotional disorders were randomly assigned to treatment (n=18) and control (n=16) groups. The treatment group and their parents received 15 sessions of UP-C. Negative Affect Schedule for Children (PANASNA- C), Children’s Anxiety Sensitivity Index (CASI), Anxiety Control Questionnaire-Children (ACQ-C) were carried out in all phases (pre-treatment, post-treatment, 3 and 8 months follow- up). The results showed that following UP-C, negative affect (hedges’g=2.01) and anxiety sensitivity (hedges’g=1.05) were significantly reduced, and perceived control (hedges’g= –2.36) was significantly improved. The results remained relatively constant during the follow-ups. Findings provide evidence that the UP-C has significant effect on negative affect, anxiety sensitivity and perceived control as roots of emotional disorders.