Inborn errors of metabolism (IEMs) refer to rare heterogeneous genetic disorders with various clinical manifestations that can cause serious physical and psychological sequelae. Results of previous studies on the impact of an IEM on health-related quality of life (HR-QoL) were incongruent and only few studies considered more broadly the psychological well-being of children with IEM and their families. Our objectives were to examine: (1) the impact of the IEM severity on the HR-QoL and psychological functioning of patients and their parents at baseline; and (2) its evolution over time; and (3) the correlation between parental and children's perspectives. Methods: The sample included 69 pediatric patients (mean age = 7.55 y, SD = 4.59) with evaluations at baseline and after one year. We collected data on HR-QoL, child mental health and emotional regulation as well as on parental mood and stress using different validated questionnaires. IEM severity was rated by a clinician through the biological subdomain of the pediatric INTERMED instrument. Results: Two groups of patients based on IEM severity scores were created (n = 31 with low and n = 38 with moderate/high IEM severity). The two groups differed with respect to age, diet and supplement intake. IEM severity had an impact on HR-QoL and behavioral symptoms in children, as well as on HR-QoL and stress in parents. For patients with moderate/high IEM severity, child and parental HR-QoL improved after 1-year of follow-up. We did not observe any significant difference between evaluations by patients versus parents. Conclusions: Our findings demonstrate that moderate/high IEM severity altered child and parental psychological well-being, but also revealed a significant improvement after one-year follow-up. This observation suggests that patients with a moderate/high IEM severity and their families benefit from the care of an interdisciplinary team including a child psychologist specialized in IEMs. Moreover, in patients with higher IEM severity there may also be more room for improvement compared to patients with low IEM severity. Future studies should focus on observations over a larger time span, particularly during adolescence, and should include objective measurements.