Control of the rail freight transportation is the comprehensive task. It requires the problem-solving and research in the field of navigation, guidance, and control of multiple moving objects. One of these problems is the problem of trajectory planning for rail freight shipping. The trajectory planning for carriage of goods by rail demands the collaborative distributed decision making and solution to specific practical problems such as the multi-agent coordination perception and coordination control of multiple moving objects, and many others. The report focuses on the trajectory planning and optimization, and more specifically: decision making to better choice the trajectory for the rail shipping in cases where dispatch and destination stations belong to the various railway territorial departments – various local control and management areas. The report focuses on this problem-solving consideration. The probability approach is applied in the paper presented to the trajectory planning and trajectory optimization. The results obtained can be used for the rail traffic planning and rail traffic control.