Abstract Background According to studies of phenylketonuria (PKU), the Brazilian population’s metabolic control shows unsatisfactory indexes from childhood. Research on patients’ perceived difficulties or barriers to adherence to treatment can help us to comprehend how these outcomes are associated. The present study aimed to: (1) describe the development of an inventory for identifying the most frequent and relevant perceived barriers to PKU treatment from the perspective of patients, caregivers, and healthcare professionals; (2) evaluate certain psychometric characteristics of the new measure; and, (3) explore potential predictors (sociodemographic and medical characteristics) that may contribute to increasing the number of perceived barriers and examine whether the number of barriers is associated with the degree of adherence shown by the patient. Results Participants in the study were 23 patients with PKU (M age = 18.0 years; SD = 7.3; range 6 to 34 years; 69% early-treated) in classical (n = 11) and mild (n = 12) form, and 11 caregivers. The inventory, developed to ascertain perceived barriers to treatment, was completed by patients (≥ 13 years) and caregivers of patients aged 6 to 17 years. Analyses were conducted to investigate whether barrier inventory scores were associated with adherence to treatment as measured by phenylalanine levels in patients’ medical records. Scores on the inventory differed across the patient age groups: adolescents had lower scores (i.e. reported fewer barriers) compared with those of adults (U = 8.000, p = 0.008); patients with better recent metabolic control also reported fewer perceived barriers than did patients with poor adherence (U = 20.000, p = 0.009); and the number of perceived barriers was positively associated with recent blood phenylalanine concentration (Kendall’s tau_b = 0.41; p = 0.001). Conclusions These results suggest that the inventory has merit in assessing perceived barriers and support the need for further research on barriers perceived by PKU patients.