Marjan Fekonja was born in Maribor in 1947, where he also earned a diploma at the School of Law. He graduated from the Faculty of Political Science in Zagreb, where he obtained a teaching degree in defence and security studies, and later, a master's degree in defence studies.

His worked at Metalna Maribor, DEM Maribor, and the regional headquarters of the Territorial Defence. From 1990 he was employed by the Ministry of Defence, where he was responsible for various tasks, and also worked as advisor to the Minister.

As a member of the Territorial Defence of the Republic of Slovenia, he organised and led the Manoeuvre Structure of National Defence for Eastern Štajerska in 1990. In 1991, he was a member of a coordination group that ran defence preparations and was engaged in the Independence War. During his time at the Ministry of Defence, he received a number of awards, in 2005 he was decorated with the Silver Order of Freedom of the Republic of Slovenia.