The objective of this review was to provide guidelines regarding the diagnosis, treatment, and prevention of the most common infectious diseases in children during natural disasters, including floods such as those that occurred in the summer of 2017 in Peru. This instrument should be used by physicians and health personnel working in primary health care. The management of diarrheal, respiratory, skin, and eye diseases, vector-transmitted diseases such as dengue, chikungunya, and Zika, and zoonoses such as leptospirosis is discussed. Emphasis is placed on the essential aspects of health education for the population, particularly preventive health, including the use of potable water, breastfeeding, immunization, hand washing, and vector control.