Background Neutropenic enterocolitis (NEC) is a dreaded complication of chemotherapy. There is scant literature regarding incidence, clinical features, and determinants. The understanding of gut dysbiosis in NEC and pediatric cancer is evolving. Methods Pediatric cancer patients with neutropenia and gastrointestinal symptoms were evaluated for NEC with CECT abdomen. Clinical, imaging, and laboratory features were analysed. Fecal samples were analysed for fecal calprotectin by sandwich ELISA and gut microbiota by conventional culture and compared with healthy controls and children without NEC. Results NEC was diagnosed in 44 children based on clinical and imaging features with incidence of 7.4% (Four had recurrent episodes). Common manifestations included fever(98%), pain abdomen(88%), and diarrhoea(83%). Hypoalbuminemia was observed in 78% patients. Large bowel involvement(94%) with diffuse bowel involvement(63%) and pancolitis(64%) were common. Fecal calprotectin was significantly elevated in NEC group than non-NEC group and healthy controls (median 87, 53, and 42 µg/g respectively). Higher degree of gut dysbiosis was observed in children with NEC with higher isolation of Bacteroides and infrequent isolation of Lactobacilli.. Mortality rate of 23% was observed. Only presence of free fluid predicted higher mortality. Though levels of fecal calprotectin and gut dysbiosis were higher in NEC, they didn’t increase mortality. Isolation of Bacteroides and absence of Lactobacilli predicted longer duration of intravenous alimentation. Conclusion NEC caused significant morbidity and mortality in pediatric cancer patients. Gut dysbiosis was significantly higher in NEC group suggesting role in pathogenesis and influencing outcome. This highlights role of targeted interventions towards gut dysbiosis like prebiotics and probiotics.