In the depopulated areas in Japan, since the major public transportation companies are withdrawing their routes, local governments are increasing their operation of regional public transportation systems. This is because most public transportation companies cannot generate adequate revenues. This has led to a shift to major public transport. Thus, the government has allocated large subsidies to public transport systems instead of the financially independent regional public transport systems. In addition, the proportion of older people in Japan continues to increase, and this is becoming a severe problem. Also, the employees of regional public transportation systems are aging, and the frequency of health-related accidents in Japan has increased. Therefore, in this paper, we propose a system that integrates the management of employee health care with the digitization of operation management through digital transformation (DX). The methods and procedures of operation management are strictly defined by law. To perform operation management, a Japanese national qualification is required. Therefore, we propose three mobile applications based on the roles, and the cloud containing multiple servers and databases on AWS. To handle employees’ information and health data, they are encrypted before stored in the cloud, where the overhead time due to encryption is important. An evaluation was performed to verify the performance of the proposed system, and the results showed that the overhead time is small and has almost no impact and that the proposed system is practical enough to be used for actual operation management.