We investigated relationships between the perception of organizational climate with gender equity and psychological health among 94 women and 211 men in a Japanese private university in 2015 using the Copenhagen Burnout Inventory (i.e., personal, work-related and student-related burnout). Perceptions of organizational climate with respect to gender equity were measured with two scales including organizational engagement with a gender equal society in the workplace (consisting of three domains of ‘Women utilization', ‘Organizational promotion of gender equal society' and ‘Consultation service'); and a gender inequality in academia scale that had been previously developed. Multivariable linear models demonstrated significant statistical interactions between gender and perceptions of organizational climate; ‘Women utilization' or lack of ‘Inequality in academia' alleviated burnout only in women. In consequence of this gender difference, when ‘Women utilization' was at a lower level, both personal ( p =.038) and work-related ( p =.010) burnout scores were higher in women, and the student-related burnout score was lower in women when they perceived less inequality in academia than in men ( p =.030). As such, it is suggested organizational fairness for gender equity may be a useful tool to help mitigate psychological burnout among women in academia.