Abstract Background Children and adolescents in mental healthcare often perceive their care needs and necessary treatment differently from their clinicians. As such discordance between young patients and clinicians may obstruct treatment adherence and compromise treatment outcomes, it is important to understand the factors associated with it. We therefore investigated the factors associated with patient–clinician discordance with regard to care needs in various areas of functioning. Methods A cross-sectional study involving 244 children/adolescents aged 6–18 participating with their clinicians in treatment at a specialized mental healthcare center. As a previous study conducted by our research group had found the greatest patient–clinician discordance in three CANSAS care needs—“mental health problems,” “information regarding diagnosis and/or treatment,” and “making and/or keeping friends”—we used univariable and multivariable statistics to investigate the factors associated with discordance regarding these three care needs. Results patient–clinician discordance on the three CANSAS items was associated with child, parent, and family/social-context factors. Three variables were significant in each of the three final multivariable models: dangerous behavior towards self (child level); severity of psychiatric problems of the parent (parent level); and growing up in a single-parent household (family/social-context level). Conclusions To deliver treatment most effectively and to prevent drop-out, it is important during diagnostic assessment and treatment planning to address the patient’s care needs at all three levels: child, parent and family/social context.