To discuss clinical diagnosis and treatment of cow’s milk protein allergy and cow’s milk protein-induced FPIES (food protein induced enterocolitis syndrome). Methods We retrospectively analyzed clinical data of one infant with milk protein allergy-induced FPIES. Results A 67 days old female on mixed breast and formula feeding developed recurrent diarrhea, abdominal distension, vomiting, mucousy and bloody stools, feeding difficulty, anemia, and failure to thrive since 2 weeks after birth. Laboratory studies showed anemia, increased CRP level and elevation of peripheral white blood count and eosinophil proportion. Milk-specific IgE was negative. She was previously hospitalized 4 times, all with admitting diagnosis of “necrotizing enterocolitis”. We treated her with milk protein elimination for 4 weeks and all symptoms were resolved. Milk protein rechallenge test was positive, consistent with clinical features of cow’s milk protein allergy-induced infant FPIES. Conclusions Cow’s milk protein allergy and cow’s milk protein-induced FPIES can present with non-specific and variable clinical symptoms and signs, and should be considered in the differential diagnosis.