Background: Febrile neutropenia is a common complication of anti-cancer chemotherapy. Invasive fungal infections are found mostly after prolonged neutropenia. Early diagnosis and treatment of these infections are of crucial importance. Hence, there is a need to identify the common causative organisms of fungal sepsis in children and our primary objective was to diagnose invasive fungal infections in children of febrile neutropenia and identify the common fungal etiological agents with clinical profile.Methods: This study was done as observational, cross-sectional study for 18 months at the department of microbiology, Lady Hardinge Medical College and department of pediatrics, Kalawati Saran Children’s Hospital. All children less than 18 years of age clinically suspected to have invasive fungal infection with absolute neutrophil count <500 /ml, with fever not responding to antibiotics for more than 3-4 days were included in the study.Results: Hospitalization ≥7 days (100%) was the most common associated risk factor, followed by neutropenia (100%), immunodeficiency (100%), cytotoxic drugs (87.27%) and malignancies (87.27%). Other less commonly associated risk factors were hyperalimentation (23.64%), residence near a construction site (23.64%), presence of urinary catheters (10.91%) and HIV positivity (9.09%). Around 54.54% of sputum samples were positive for fungal culture. A lower positivity was seen in blood culture (14.54%).Conclusions: Candida spp., Aspergillus spp. and Pneumocystis remain the primary fungal pathogens in this patient population. Early clinical suspicion followed by prompt sampling and evaluation for fungal infections may aid in timely diagnosis and reduction of mortality of these patients.