Supply chain problems can have a significant impact on a company’s profitability and customer satisfaction. Addressing these challenges often involves a combination of strategic planning, process optimization, and the use of advanced technologies to streamline operations and enhance supply chain resilience. A good supply chain design provides an optimal platform for the efficient supply chain management. This paper analyzes the three-level supply chain problem: goods are transported from suppliers to distribution centers, where goods are repackaged and shipped to customer zones. This problem is formulated in the form of the quadratic binary programming. In this work, we introduce a genetic algorithm to find the optimal solution and demonstrate the effectiveness of our proposed algorithm through a set of different scale problems and compare its results with those obtained by CPLEX.