Di sebabkan penglibatan Croatia dan Serbia, terdapat satu perdebatan panjang sama ada konflik ini merupakan sebuah perang saudara atau sebuah perang pencerobohan di Bosnia oleh negara-negara berjiran. Ahli akademik, Steven Burg dan Paul Shoup brhujah bawaha :

From the outset, the nature of the war in Bosnia-Herzegovina was subject to conflicting interpretations. These were rooted not only in objective facts on the ground, but in the political interests of those articulating them.

—Steven L. Burg and Paul S. Shoup, The War in Bosnia-Herzegovina[137]

Pada sisi yang lain, perang ini dilihat sebagai "sebuah kes perang saudara yang jelas – iaitu, perang dalaman antara kumpulan-kumpulan yang tidak bersetuju dengan pengaturan pembahagian kuasa".[137]

David Campbell is critical of narratives about "civil war", which he argues often involve what he terms "moral levelling", in which all sides are "said to be equally guilty of atrocities", and "emphasise credible Serb fears as a rationale for their actions".[201]

In contrast to the civil war explanation, Bosniaks, many Croats, western politicians and human rights organizations claimed that the war was a war of Serbian and Croatian aggression based on the Karađorđevo and Graz agreements, while Serbs often considered it a civil war.

—Steven L. Burg and Paul S. Shoup, The War in Bosnia-Herzegovina[137]

Bosnian Serbs and Bosnian Croats enjoyed substantial political and military backing from Serbia and Croatia, and the decision to grant Bosnia diplomatic recognition also had implications for the international interpretation of the conflict. As Burg and Shoup state:

From the perspective of international diplomacy and law...the international decision to recognize the independence of Bosnia-Herzegovina and grant it membership in the United Nations provided a basis for defining the war as a case of external aggression by both Serbia and Croatia. With respect to Serbia, the further case could be made that the Bosnian Serb army was under the de facto command of the Yugoslav army and was therefore an instrument of external aggression. With respect to Croatia, regular Croatian army forces violated the territorial integrity of Bosnia-Herzegovina, lending further evidence in support of the view that this was a case of aggression.

—Steven L. Burg and Paul S. Shoup, The War in Bosnia-Herzegovina[137]

Sumantra Bose, meanwhile, argues that it is possible to characterise the Bosnian War as a civil war, without necessarily agreeing with the narrative of Serb and Croat nationalists. He states that while "all episodes of severe violence have been sparked by 'external' events and forces, local society too has been deeply implicated in that violence" and therefore argues that "it makes relatively more sense to regard the 1992–95 conflict in Bosnia as a 'civil war' – albeit obviously with a vital dimension that is territorially external to Bosnia".[202]

In 2010, Bosnian Commander Ejup Ganić was detained in London on a Serbian extradition request for alleged war crimes. Judge Timothy Workman decided that Ganić should be released after ruling that Serbia's request was "politically motivated". In his decision, he characterised the Bosnian War to have been an international armed conflict as Bosnia had declared independence on 3 March 1992.[203]

Academic Mary Kaldor argues that the Bosnian War is an example of what she terms new wars, which are neither civil nor inter-state, but rather combine elements of both.[204]