Background The use of a prophylactic antibiotic in an amputation surgery is a key element for the successful recovery of the patient. We aim to determine, from the perspective of the Colombian health system, the cost-effectiveness of administering a prophylactic antibiotic among patients undergoing lower limb amputation due to diabetes or vascular illness in Colombia. Methods A decision tree was constructed to compare the use and nonuse of a prophylactic antibiotic. The probabilities of transition were obtained from studies identified from a systematic review of the clinical literature. The chosen health outcome was reduction in mortality due to prevention of infection. The costs were measured by expert consensus using the standard case methodology, and the resource valuation was carried out using national-level pricing manuals. Deterministic sensitivity, scenarios, and probabilistic analyses were conducted. Results In the base case, the use of a prophylactic antibiotic compared with nonuse was a dominant strategy. This result was consistent when considering different types of medications and when modifying most of the variables in the model. The use of a prophylactic antibiotic ceases to be dominant when the probability of infection is greater than 48%. Conclusions The administration of a prophylactic antibiotic was a dominant strategy, which is a conclusion that holds in most cases examined; therefore, it is unlikely that the uncertainty around the estimation of costs and benefits change the results. We recommend creating policies oriented toward promoting the use of a prophylactic antibiotic during amputation surgery in Colombia. © 2016 Elsevier Inc.