Introduction: Work style reform of medical doctors is now an actively discussed matter in Japan. There is also the problem of how to balance the management of legal working hours and the value of medical education in junior residency programs. In particular night and holiday shifts in emergency departments are one of the most important causes of working hour elongation for junior residents. We tried to construct a legally appropriate management method to control their working hours including night and holiday shifts. Method: One-Month Variable Working Hours System and two-shift system were applied to labor management in the medical residency program. Night and holiday working hours were included in regular working hours. Day-time working hours were adjusted to the weekly schedule of each clinical department to cover most of its daily work. Result: Overtime working hours of all residents, including the night and holyday shifts, were managed within the legal limits of 45 hours a month, unless additional overtime work was required. Discussion: Managing worktime through the use of the One-Month Variable Working Hours System is thought to be feasible. In the junior residency program, night and holiday shifts in the emergency department could also be balanced.