This paper discusses the legal rules governing the time limits of application of criminal legislation in adjudicating international crimes before the courts in Bosnia and Herzegovina. The author points out to the existence of two different criminal law regimes which are used against the criminal offenders: the first one is used by the courts of the B&H Entities and the Brčko District, where these rules are applied consistently and the criminal offenders are awarded prison sentences within the penal framework envisaged in earlier criminal codes, including the so-called interim laws; the second one is applied by the Court of Bosnia and Herzegovina which, in compliance with the B&H Criminal Code of 2003, may award long-term imprisonment of up to 45 years for the commission of these criminal offences even though this penalty did not exist in the B&H criminal law at the time when the acts were committed. In particular, the paper focuses on the legal issue arising from the European Court of Human Rights (ECtHR) judgment in Maktouf and Damjanovic vs. Bosnia and Herzegovina (18 July 2013), where the Court established a violation of Article 7, paragraph 1 of the European Convention on Human Rights (ECHR). The author discusses the common standpoint that the judgment removed all misunderstandings concerning the application of these rules; considering that such conception is unjustified, the author identifies a number of other outstanding problems which occurred in the application of these rules after rendering the above judgment. The author specifically considered the criminal provision on Crimes against Humanity as envisaged in Article 172 of the B&H Criminal Code, which the B&H Court regards as a new criminal offence which is envisaged in Article 7, paragraph 2 of the ECHR. The author believes that such application of this criminal offence is unjustified. Upon providing an analysis of the elements of crime constituting the legal nature of this criminal offence, the author concludes that it is not a completely new criminal offence; for this reason, it may not be subject to this provision, i.e. the punishment shall not be imposed by relying on the basis of general principles of international law.