Ample research has supported the detrimental impact of burnout on the well-being of resident doctors. However, the mechanisms accounting for this influence remain unclear. Consequently, this study analysed for the first time the degree of burnout as well as its evolution throughout the residency period and tested the mediational role of resiliency in the relationship between burnout and its subscales and well-being in a sample of 237 Spanish residents of different specialties from Spanish hospitals. Participants were administered the Maslach Burnout Inventory, the Connor Davidson Resilience Scale and the short-version scale of Subjective Well-being. From the total sample of residents, 48.9% reported high levels of total burnout, 53.6% in the subscale of emotional burnout and 74.7% in depersonalization. Additionally, burnout levels increased as the residency period progressed, and resilience mediated the relationship between burnout and subjective well-being level. Such findings suggest resilience as a protector factor against burnout that should be included in prevention programs.