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Abstract Background Despite enormous advances in therapy, phenylketonuria (PKU) remains an incurable, inherited metabolic disease requiring life‐long treatment with potential to negatively impact quality of life and psychological well‐being. Therefore, the aim of this study was to screen early diagnosed and continuously treated children with PKU on psychological strengths and behavioral difficulties. Methods Evaluation of psychological strengths and behavioral difficulties in 49 patients with PKU (23f, 2‐17 years) by Strengths and Difficulties Questionnaire (SDQ; self‐report 11‐17 years and parent‐report 2‐17 years). Comparison to age, sex and BMI‐matched healthy controls (n = 98; 46f). Results In patients with PKU and healthy controls median SDQ Total Difficulties Score and median scores of subscales were within the normal range in parent‐ and self‐report, irrespective of sex and age group (children 2‐10 years, adolescents 11‐17 years). No influence of long‐term metabolic control in PKU on SDQ could be revealed. The 2‐ to 10‐year‐old boys with PKU showed significantly higher scores in Prosocial Behavior compared to their healthy peers (P = .032). Likewise, adolescent boys with PKU showed fewer Conduct Problems (parent‐report, P = .006). Adolescent girls with PKU rated themselves more often as abnormal in the subscale Emotional Problems compared to their healthy peers (P = .041). This subscale was also responsible for a significantly different Total SDQ Difficulties Score between patients and their parents' report (P = .008). Discussion SDQ represents a suitable instrument within the care for patients with PKU. Specific aspects, however, require separate consideration and evaluation with respect to this chronic disease. Special attention should be paid on adolescent PKU girls who seem to be at risk to develop emotional problem.