Background: In children with intestinal failure (IF), supportive management for preventing chronic malnutrition that results in hematological complications is highly important. Careful treatment including that for psychogenic problems and medical management is required in adolescent patients. Case presentation: A 12-year-old boy who underwent gastric wedge resection was transferred to our hospital because of chronic loss of appetite, vomiting, growth failure, and weight loss. As he was able to ingest orally, we tried to restore his general condition and increase his weight by maintaining additional nutritional supply through peripheral parenteral nutrition ( PN). However, continuous vomiting, weight loss, and superior mesenteric artery syndrome persisted because of low treatment compliance. The findings of hyponatremia and bicytopenia did not improve. Bone marrow biopsy was performed, and it revealed copper deficiency. PN was increased via the central route, and additional micronutrient agents, including copper, were administered. In particular, invasive diagnosis and treatment, and adequate education improved the treatment compliance of the child. Since then, he avoided intake of large amounts of beverages and thus no longer had repeated vomiting and weight loss. His copper deficiency and bicytopenia improved, and his weight and dietary intake also increased. Conclusions: We confirmed that treatment compliance is important in pediatric patients with malnutrition. In chronic malnutrition, attention should also be paid to deficiency of micronutrients such as copper, which can lead to hematologic problems. In patients with pediatric IF, a multidisciplinary approach such as medical, surgical, and psychological management will prevent further complications and provide better therapeutic results.