Combine green beans and water in a skillet over medium-high heat. Cover and cook, stirring occasionally, until beans are tender crisp, 4 to 5 minutes. Add ginger, garlic, and sesame oil; cook, stirring frequently, until garlic is lightly browned, 1 to 2 minutes.
Mix soy sauce, rice vinegar, sugar, and red pepper flakes together in a small bowl. Pour over beans and cook until sauce thickens enough to coat beans, 3 to 5 minutes.
