Junkelmann was born in Munich to the art historian Erich Junkelmann and his wife Charlotte. The family soon moved to Schleißheim and took residence in theLustheim_Palace, where Junkelmann spent his youth. He graduated 1969 from the Dom-Gymnasium Freising (high school) and started to study history atLudwig Maximilian University of Munich in 1971. In 1979 he received his PhD for a thesis on the military achievements ofMaximilian II (1662–1726) (original title: Kurfürst Max Emanuel von Bayern als Feldherr). After that he worked as an associate member of staff at the university and for theBayerisches Armeemuseum (military museum) inIngolstadt.
In the 1980s Junkelmann became well known in Germany for his work inexperimental archeology. He reconstructed and tested Roman weapons and army gear. In 1985 in connection with the 2000 year celebration of the city ofAugsburg he organized a largeexperimental reenactment of the life and work conditions ofRoman legionaries. The experiment consisted of a month-long march fromVerona toAugsburg including a crossing of theAlps. For the complete trip the original Roman army gear and equipment was used and the typical legionary tasks were performed. Later Junkelmann went on to perform a similar experiments for the Roman cavalry. He authored several books and documentaries on his archeological experiments. In 1997 he was awarded theCeram Prize for his book on the nutrition of Roman soldiers (original title:Panis militaris: Die Ernährung des römischen Soldaten oder der Grundstoff der Macht).
Römische Kampf- und Turnierrüstungen, Sammlung Axel Guttmann (zusammen mit Hermann Born), Verlag Philipp von Zabern, Mainz 1997ISBN3-8053-1668-2
Arte & Marte Theatrum belli. Die Schlacht bei Höchstädt 1704 und die Schlösser von Schleißheim und Blenheim, Bautz, Traugott, Herzfeld 2000ISBN3-88309-083-2
Aus dem Füllhorn Roms. 34 Originalrezepte aus der römischen Küche, Verlag Philipp von Zabern, Mainz 2000ISBN3-8053-2686-6
Das greulichste Spectaculum. Die Schlacht von Höchstädt 1704. Hefte zur Bayerischen Geschichte und Kultur Bd. 30, hrsg. vom Haus der Bayerischen Geschichte 2004,ISBN3-927233-90-0
Bilder aus der deutschen Vergangenheit. Der deutsche Soldat (Bayerischer Rundfunk, 1986 – zahlreiche Wiederholungen)
Der Römerschatz von Sorviodurum. Das Gäubodenmuseum Straubing (Landesstelle für die nichtstaatlichen Museen/Bayerischer Rundfunk, 1994)
Gerichte mit Geschichte. Römische Küche im alten Bayern. Film von Werner Teufl und Dr. Marcus Junkelmann (Bayerisches Fernsehen, 2000 – auch als Video)
