A number of combinatorial optimization problems in machine learning can be described as the problem of minimizing a submodular function. It is known that the unconstrained submodular minimization problem can be solved in strongly polynomial time. However, additional constraints make the problem intractable in many settings. In this paper, we discuss the submodular minimization under a size constraint, which is NP-hard, and generalizes the densest subgraph problem and the uniform graph partitioning problem. Because of NP-hardness, it is difficult to compute an optimal solution even for a prescribed size constraint. In our approach, we do not give approximation algorithms. Instead, the proposed algorithm computes optimal solutions for some of possible size constraints in polynomial time. Our algorithm utilizes the basic polyhedral theory associated with submodular functions. Additionally, we evaluate the performance of the proposed algorithm through computational experiments.