A working alliance (WA) is a multidimensional construct signifying a collaborative relationship between a client and a therapist. Systematic reviews of therapies to treat depression and anxiety, almost exclusively in adults, show WA is essential across psychotherapies. However, there are critical gaps in our understanding of the importance of WA in low-intensity therapies for young people with depression and anxiety. Here, we describe an initiative to explore the effect of WA on anxiety and depression outcomes in youth aged 14–24 years through a scoping review and stakeholders’ consultations (N = 32). We analysed 27 studies; most were done in high-income countries and evaluated one-on-one in-person therapies (18/27). The review shows that optimal WA is associated with improvements in: relationships, self-esteem, positive coping strategies, optimism, treatment adherence, and emotional regulation. Young people with lived experience expressed that: a favourable therapy environment, regular meetings, collaborative goal setting and confidentiality were vital in forming and maintaining a functional WA. For a clinician, setting boundaries, maintaining confidentiality, excellent communication skills, being non-judgmental, and empathy were considered essential for facilitating a functional WA. Overall, a functional WA was recognised as an active ingredient in psychotherapies targeting anxiety and depression in young people aged 14–24. Although more research is needed to understand WA’s influence in managing anxiety and depression in young people, we recommend routine evaluation of WA. Furthermore, there is an urgent need to identify strategies that promote WA in psychotherapies to optimise the treatment of anxiety and depression in young people.