Taxation of the financial sector covers a wide range of topics, including but not limited to the taxation of financial institutions and financial services, but also related regulation of each of the financial markets. The failure of financial markets called for a need of a comprehensive approach to the taxation of the financial sector while taking into account the current and potential concepts of corporate income tax and valued-added tax that themselves may pose some problems. This also includes the issue of financial transaction and financial activities taxation and bank levy. The importance of this topic in the Czech Republic will be underlined in the upcoming general elections. The aim of this paper is to design a system of rational taxation of the Czech financial sector for the upcoming period, while considering the Czech specifics.