Abstract Background Intestinal obstruction (IO) is a common pediatric surgical emergency in sub-Saharan Africa with high morbidity and mortality, but little is known about its etiopathogenesis in Malawi. Methods Retrospective analysis of patients seen from February 2012 to June 2014 at Kamuzu Central Hospital in Lilongwe, Malawi (n = 3,407). Pediatric patients with IO were analyzed (n = 130). Results Overall, 57% of patients were male with a mean age of 3.5 ± 4.1 years. A total of 52% of patients underwent operative intervention. The overall mortality rate was 3%. Leading causes of IO were Hirschprung's 29%, anorectal malformation 18%, and intussusception 4%. Neonates and patients with congenital causes of IO underwent surgery less frequently than infants and/or children and patients with acquired causes, respectively. These groups also demonstrated increased number of days from admission to surgery. Conclusions Increasing pediatric-specific surgical education and/or training and expanding access to resources may improve mortality after IO in poor medical communities within sub-Saharan Africa