Objectives The Japanese government partially enacted the “Work Style Reform Bill” in 2019. The National Center for Child Health and Development (NCCHD) introduced an Overnight Call Shift (OCS) system for pediatrician training. We conducted a follow‐up survey in 2019 to investigate the long‐term effectiveness of the OCS system to improve the pediatric residents' mental wellness at NCCHD. Methods We conducted a questionnaire‐based cross‐sectional survey for pediatric residents in 2019 to compare the data with those of the previous survey in 2012. The questionnaire includes demographic data, working conditions data, and mental wellness assessment by the Center for Epidemiologic Studies Depression scale (CES‐D) and the Maslach Burnout Inventory (MBI). Results The collection rate for the 2019 survey was 94.5% (37 participants/39 eligible). Compared to 2012, there were no significant changes in demographic data and working hours, a significant increase by about 30% in residents who took daytime off after night work, about 10% decrease in residents who scored 16 and above on the CES‐D, and a significant decrease in the mean score for depersonalization (DP) in the MBI. Multiple regression analyses showed that daytime off after night work was the decreasing factor for CES‐D and Emotional exhaustion (EE). Conclusions The overnight shiftwork system shortened the pediatric residents' duty hours somewhat, and imposed an impact on the pediatric residents' mental wellness.