Presently, an increasing human population, customer consumption, and global market competition result in the reduction of natural resources and growing environmental damage. Therefore, the current practice in the use of resources is not sustainable. The production companies have to focus not only on cost-effective and profitable operation, but at the same time environmentally friendly and sustainable production in order to increase competitiveness. New innovative technologies are required, improving the efficiency of the processes and the optimization of global supply chains (GSC) in order to establish sustainability in environmental, social, and economic aspects. The aim of the study is the GSCs’ optimization, which means forming the optimal combination of the chain members (suppliers, final assemblers, service providers) to achieve cost-effective, time-effective, and sustainable operation. This study introduces an elaborated single- and multi-objective optimization method, including the objective functions (cost, lead time) and design constraints (production and service capacities; volume of inventories; flexibility and sustainability of the chain members). Based on the elaborated method, software has been developed for the optimization of sustainable GSCs. The significance and novelty of the developed method and software is that the chain members have been required to fulfill the sustainability design constraint built into the software. A real case study is introduced, for the optimal design of a sustainable GSC, to confirm that our developed optimization method and software can be applied effectively in practice for the optimization of both profitable and sustainable GSCs.