The paper deals with the development of taxing banks in the Czech Republic before and after its membership in the European Union from 2001 to 2012. In particular, it covers taxation of taxes on corporate income, and the value-added tax. The aim of this paper is to propose a modification in the taxation of banks in the Czech Republic taking into account their specificities and economic position in relation to their contribution to public budgets. Methods, analysis and description of scientific literature and national legislation were used, including mathematical and statistical methods to describe the time series of selected indicators. It is proposed to increase the income tax rate for the banking sector or the introduction of a bank tax, supporting a possible future EU proposal to introduce a tax on financial transactions.