While it is well established that women have lower pay than men, it is not known if women and men perceive the justice of a pay setting process differently or if perceptions of justice differ depending on the gender of the supervisor. The aim of this study was to investigate differences between women and men employees, who have a woman or man as pay-setting supervisor, in perceived pay-related justice as well as actual pay level and pay raise (in relative and absolute levels). Questionnaire data were collected from 841 employees in a Swedish private sector company that has implemented a new pay-for-performance system. 2 (employee’s gender) * 2 (supervisor’s gender) MANOVAs indicate that women experienced higher levels of perceived pay justice than men. There was no gender difference in relative pay increase, whereas men, on average, had a higher pay-level and absolute pay increase than women. On average, men pay-setting supervisors gave a higher pay-increase than women pay-setting supervisors. There only significant interaction effects was for pay level. The data derives from one company that has worked hard to implement a new pay-setting system. The study needs replication in other organizational contexts as well as in nationally representable samples. Implementing pay-for-performance systems has the potential to create a more gender equal pay-setting process. This is one of few studies investigating gender equity in pay-related justice and the potential effects of the pay-setting supervisors’ gender in a performance-based pay-system.