Anorectal malformation, a congenital defect is usually detected at birth and managed by a multispeciality team in a tertiary care hospital. We present a case of a five day old neonate, born in a remote village in South Sudan, who presented in a critical condition to our field hospital and was managed with basic resources. A 5 day old neonate was detected with imperforate anus and presented to our hospital on day 5 with abdominal distension, severe dehydration, tachycardia and tachypnoea. Radiographic investigations revealed findings suggestive of a high ano-rectal malformation. The neonate underwent an emergency exploratory Laparotomy with diversion double barrel Colostomy in a set up catering for adult combatants. The neonate gradually improved before developing burst abdomen managed with emergency wound closure. The neonate gradually accepted breast feeds and was discharged for subsequent need for definitive surgery. This was a challenging surgery with respect to the resources available at a field hospital catering to adult combatants.