Previous research has pointed to the significant role of the characteristics of companies and workplaces in explaining differences in individuals’ income. The gender pay gap (GPG) is most often analysed from the perspective of the personal characteristics of men and women and the characteristics of their work, but little attention has yet been paid to organisational characteristics. In this study, we focus on this less explored context influencing the GPG and ask the following questions: (1) What organisational characteristics are significant and how are they related to the average GPG in the company/workplace? (2) Do these characteristics act differently in the public and private sectors of the labour market? (3) Are the differences found according to organisational characteristics of a long-term nature? and (4) Have there been significant changes in connection with the Covid-19 pandemic? We use data from the Information System on Average Earnings (ISPV) for the years 2010, 2020, and 2021 and apply multiple linear regression, where the dependent variable is the GPG in the company/at the workplace. We conclude that the GPG is significantly lower in the public sector than in the private sector. The classification of economic activities by NACE, the size of the company/workplace, the degree of gender segregation into positions within workplaces, but also the region and other characteristics prove to be important. These effects appear to be long-term but more subtle changes can be observed between the private and public sectors. The analysis confirms that organisational characteristics are significant when analysing the GPG and points to other areas of research that need to be explored.