A system for, and method of, configuring border gateway selection for transit traffic flows in a computer network. In one embodiment, the system includes: (1) a border gateway modeler that builds a model of cooperating border gateways, the model including capacities of the border gateways and (2) a traffic flow optimizer, associated with the border gateway modeler, that initially assigns traffic to the border gateways in accordance with a generalized assignment problem and subsequently reassigns the traffic to the border gateways based on cost until the capacities are respected.