The Unified Protocol for Transdiagnostic Treatment of Emotional Disorders in Adolescents (UP-A) has been shown to be effective for reducing symptoms of anxiety and depression in adolescents with emotional disorders. Internet-delivered psychological treatments have great potential to improve access to evidence-based psychological therapy since they are associated with reduced human and economic costs and less social stigma. Recently, our group developed an online version of the UP-A (the iUP-A) for the treatment of emotional disorders in adolescents. The aim of this pilot trial was to test the clinical utility of the iUP-A in a small sample (n = 12) of adolescents with elevated anxiety and/or depressive symptoms. Intention-to-treat and completer analyses revealed pre- to post-intervention self-reported decreases of anxiety and depressive symptoms, anxiety sensitivity, emotional avoidance, panic disorder symptoms, panic disorder severity, generalized anxiety disorder symptoms, pathological worry, and major depressive disorder symptoms. We found high feasibility and acceptability of the program with all participants and responsible parents reporting an improvement in the adolescents’ ability to cope with emotions. Results suggest that the iUP-A may provide a new approach to improve access to treatment for anxious and depressive adolescents in Spain; however, further research must be conducted before firm conclusions can be drawn.