We examined the implementation of mental health prevention programs in Japanese workplaces and the costs and benefits. A cross-sectional survey targeting mental health program staff at 11 major companies was conducted. Questionnaires explored program implementation based on the guidelines of the Japanese Ministry of Health, Labor and Welfare. Labor, materials, outsourcing costs, overheads, employee mental discomfort, and absentee numbers, and work attendance were examined. Cost-benefit analyses were conducted from company perspectives assessing net benefits per employee and returns on investment. The surveyed companies employ an average of 1,169 workers. The implementation rate of the mental health prevention programs was 66% for primary, 51% for secondary, and 60% for tertiary programs. The program’s average cost was 12,608 yen per employee and the total benefit was 19,530 yen per employee. The net benefit per employee was 6,921 yen and the return on investment was in the range of 0.27–16.85. Seven of the 11 companies gained a net benefit from the mental health programs.