The article deals with the critical assessment of the control of criminal prosecution in the legal systems of Bosnia and Herzegovina and the Republic of Croatia. For the purpose of this paper, criminal prosecution concerns only decisions to initiate, continue and discontinue criminal procedure but not to take individual investigative measures or other procedural actions. The normative and comparative methods are predominantly employed in the article to conduct a qualitative assessment of relevant provisions of criminal procedure acts of both countries. Additionally, the paper evaluates its subject through the lens of the jurisprudence of the European Court of Human Rights. Albeit the mentioned countries belong to the same legal tradition, they have adopted different legal solutions regarding the conception of the control of criminal prosecution. B&H law primarily relies on the internal control of criminal prosecution through the use of a complaint filed with the prosecutor’s office. In contrast, besides establishing judicial control of criminal prosecution, Croatian law retained subsidiary prosecution as a form of external control of prosecutorial function. While the defendant has the right to be shielded from arbitrary criminal prosecution, the injured party as a person suffering harm from a criminal offense has the right to effective criminal prosecution in the case of serious violations of his/her human rights. Hence, the article aims to establish that the nonexistence of external control of criminal prosecution in B&H law violates the mentioned rights of the defendant and those of the injured person. The article also argues that the legal solutions in Croatian law regarding the external control of criminal prosecution could be used to some extent as a model for future reform of criminal procedure in B&H. Lastly, the article highlights that subsidiary prosecution as a corrective to prosecutorial function in Croatia has its shortcomings.