Invasive gastrointestinal fungal infections are posing a serious threat to the ever-expanding population of immunocompromised children, as well as some healthy children at risk. In this narrative review, we collate and explore the etiologies and diagnostic modalities of these overlooked infections.  Currently, the conventional diagnostic approaches of histopathologic examination and culture are still considered the gold standard for diagnosis. However, these approaches may be time-consuming and have low sensitivities, which emphasizes the need for new diagnostic modalities in such life-threatening infections. Meanwhile, biomarkers that detect fungal antigens e.g. galactomannan and beta-D-glucan have been established and implemented in various clinical settings. On the other hand, novel molecular techniques have been developed and are currently subjected to further evaluation and validation. Other promising approaches such as the matrix-assisted laser desorption ionization (MALDI) and surface-enhanced resonance Raman scattering (SERRS) have proved reliable in clinical trials but still require standardization before widespread clinical application. The incorporation of standardized novel diagnostic tools would provide the necessary guidance to therapeutic approaches. Prompt treatment of IFD necessitates surgical intervention together with systemic anti-fungal agents. The most widely used agents include amphotericin B, voriconazole, and caspofungin. A high index of suspicion coupled with prompt diagnosis and judicious management can tremendously improve the survival of the vulnerable pediatric population.