Logistics is defined classically as an integrated science, which aims to solve the problem of optimal control of the movement process of various flows: physical (resources or goods), financial, informational as well as the movement of human resources. To solve the logistic problems the systematic approach to logistics is needed, i.e. investigations of logistic operations and functions in the sector of logistics. Drawing attention to the realities of economic life it is necessary to analyze the relation between uncertainty and certainty in the logistics, as well to create the algorithm for the logistics system optimization. However, the paradigm of research and logistics systems in the global economy should pay attention to the realities of the economy. This is how the authors of this paper make their research. They do research in the light of the relation between uncertainty and certainty of the logistics, creating algorithm of the logistics system optimization. To explain the mechanism of the relation of uncertainty and certainty in logistics the model of management decisions on the dismissal of staff can be successfully used. Logistics system optimization algorithm is able to provide coherent decision – making on strategic competitive alternatives directions of traffic flow, increase efficiency in terms of the functioning of logistics systems.