The working conditions during COVID-19 highlight the relevance of workers and their occupational health and well-being. The pandemic has caused adverse effects on workers and sharpened social and economic problems, such as a gender gap. In this study, with a multisector sample of 1044 Ecuadorian workers, we present a gender analysis where we evaluate how burnout can mediate the relationship between motivation and workers’ intention to leave their jobs in the COVID-19 context. To test the proposed hypothesis, structural equation model (SEM) was used. In the proposed conceptual model, turnover intention was considered as the dependent variable, the two dimensions of motivation (intrinsic and extrinsic) were the independent variables and burnout was tested as a mediating variable. Consistent with pre-COVID-19 research, our findings confirm the incidence of job motivation on burnout and turnover intention. Additionally, through Sobel’s criteria, we determine that burnout has a mediating effect between job motivation and turnover intention. In terms of gender, we find different results for female and male workers through critical ratios. Our study indicates that female and male workers’ burnout and turnover intentions levels are different when intrinsic motivation is present. In contrast to pre-COVID-19 studies that indicated no gender differences on these variables, we associate these results to gender roles in lockdown conditions during the pandemic.