A problem of scheduling freight trains in rail-rail transshipment yards is considered. It is solved at a deeper level compared to original papers dedicated to this problem: besides scheduling service slots for trains, this article additionally solves a problem of assigning every train to a railway track. A mathematical model and a solving method for this problem are given. A key feature of the given mathematical model is that it doesn’t use Boolean variables but rather operates with combinatorial objects (tuples of permutations). The solution method is also based on generation of combinatorial sets, which is quite an unusual approach for solving such problems.