Background: Burnout syndrome is very prevalent among healthcare residents. Initiatives addressing workload conditions have had limited impact on burnout. The present study aims to explore the contribution of two emotion regulation strategies, namely emotion suppression and cognitive reevaluation, to residents’ burnout, while accounting for workload factors. Methods: Participants were 105 residents (68.6% women; mean age = 27.5, SD = 3.0). They completed measures of workload, burnout, and emotion regulation. The study was cross-sectional. Results: Emotional suppression was associated with higher burnout (depersonalization scale; β = 0.20, p < 0.05, CI 0.15–2.48) and cognitive revaluation was linked to lower burnout (higher personal accomplishment; β = 0.35, p < 0.01, CI 0.16–2.56), even after controlling for demographic and workload factors. We found interaction effects between workload variables (supervisor support and number of patient hours) and emotion regulation (p < 0.05). Conclusions: The relationship between workload, emotion regulation, and burnout seems to be complex. That is, similar work conditions might generate different levels of burnout depending on the resident’s emotional regulation strategies. This might partly explain why existing initiatives based on workload changes have had a modest impact on burnout. Results also support including emotion regulation training in prevention and treatment programs targeting burnout during residency.