Invasive fungal disease (IFD) has a high incidence in patients with hematologic malignancies who have undergone hematopoietic stem cell transplantation, particularly in children. IFD increases mortality and presents multiple challenges in diagnosis and treatment. Among these fungi, Aspergillus, Candida, and Trichoderma are the main pathogens. Infections caused by these fungi usually present with nonspecific symptoms such as fever and dyspnea, further complicating the diagnosis. Invasive Candida infections can manifest as candidemia or chronic disseminated candidiasis (eg. involving the liver and spleen). The latter condition can be accompanied by localized symptoms such as right upper quadrant tenderness and abdominal pain, which further complicates the early diagnosis of IFD. The early diagnosis and effective treatment of IFD after hematopoietic stem cell transplantation for pediatric hematologic neoplasms require multiple tools to overcome clinical challenges and improve patient prognosis.