The article deals with the application of the ne bis in idem principle in the tax process. It focuses in particular on the nature of penalty payments under the Tax Code. The jurisprudence of the Supreme Courts of the Czech Republic and the European Court of Human Rights has recently raised more questions about it than gave answers. Therefore, the article focuses in particular on the analysis of their decisions and, on the basis of this, tries to define theoretical legal bases for the application of the ne bis in idem principle in relation to the imposition of a penalty payment by the tax administrator.