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Duty hour regulations have been placed in residency programs to address mental health concerns and to improve wellness. Here, we elucidate the prevalence of depressive symptoms after implementing an overnight call shift system and the factors associated with burnout or depression among residents. A sequential exploratory mixed methods study was conducted in a tertiary care pediatric and perinatal hospital in Tokyo, Japan. A total of 41 pediatric residents participated in the cross-sectional survey. We determined and compared the prevalence of depressive symptoms and the number of actual working hours before and after implementing the shift system. A follow-up focus-group interview with 4 residents was conducted to explore the factors that may trigger or prevent depression and burnout. Mean working hours significantly decreased from 75.2 hours to 64.9 hours per week. Prevalence of depressive symptoms remained similar before and after implementation of the shift system. Emotional exhaustion and depersonalization from the burnout scale were markedly associated with depression. High workload, stress intolerance, interpersonal difficulties, and generation gaps regarding work–life balance could cause burnout. Stress tolerance, workload monitoring and balancing, appropriate supervision, and peer support could prevent burnout. Although the overnight call shift system was effective in reducing working hours, its effectiveness in managing mental health issues among pediatric residents remains unclear. Resident wellness programs represent an additional strategy and they should be aimed at fostering peer support and improvement of resident–faculty interactions. Such an approach could be beneficial to the relationship between physicians of different generations with conflicting belief structures.