Salaries at Charles University are defined by an internal payroll policy.They are classified as either a contractual salary, or as a tariff salary, personal bonus, management bonus, and extra pay for difficult working conditions, overtime work, work on public holidays, night work, and weekend work. The salary includes all bonuses with the exception of the bonus for standby service.

The salary is set or agreed on an individual basis with respect to the difficulty and demands of the position, qualification requirements, performance in line with the overall level of salaries at Charles University and, in justified cases, with regard to the salary level for a specific position on the relevant labour market. The amounts of each salary component, including but not limited to the tariff salary, personal bonus, and management bonus, are defined by a salary assessment or agreed on a contractual basis.