Maintaining a young, well-educated labor force is an important strategy for regional economic development and social vitality. Based on a comparative study of China and Japan, this article aims to elicit 1) the factors that affect college students’ employment migration preference; and 2) the differences between migration preferences of students from the two countries and the possible explanations for such differences. With the use of survey data from approximately 2,000 college students in the two countries, this study identifies region of origin as a key determinant of employment migration choice in both countries. The region of origin functions as a critical point differentiating primary and secondary labor markets for individuals, whereas the first-tier region in each country is a popular work destination. A one-way bottom-up migration from lower-ranking to higher-ranking regions is revealed in our regional hierarchy model. Findings suggest that Chinese students were oriented to employment opportunities and economic well-being while Japanese students were more inclined to consider personal lifestyle and local amenities. The findings imply that reducing regional disparities in economic development and income levels in China and enhancing urban service facilities in Japan may encourage college graduates to remain in their home regions.