Distinct differences exist between public-private sector organizations with respect to the market environment and operational objectives; furthermore, among private sector businesses, organizational structures and work conditions often vary between large- and small-sized companies. Despite these obvious structural distinctions, however, sectoral differences in employees’ psychosocial risks and burnout status in national level have rarely been systematically investigated. Based on 2013 national employee survey data, 15,000 full-time employees were studied. Sector types were classified into “public,” “private enterprise-large (LE),” and “private enterprise-small and medium (SME);” based on the definition of SMEs by Taiwan Ministry of Economic Affairs, and the associations of sector types with self-reported burnout status (measured by the Chinese version of Copenhagen Burnout Inventory) were examined, taking into account other work characteristics and job instability indicators. Significantly longer working hours and higher perceived job insecurity were found among private sector employees than their public sector counterparts. With further consideration of company size, greater dissatisfaction of job control and career prospect were found among SME employees than the other two sector type workers. This study explores the pattern of public-private differences in work conditions and employees’ stress-related problems to have policy implications for supporting mechanism for disadvantaged workers in private sectors.