Two German pilots, Leutnants Otto Parschau and Kurt Wintgens, worked closely with Anthony Fokker in early 1915 during evaluation of the M.5K/MG. Wintgens is known to have downed a two-seat Morane-Saulnier Type L parasol monoplane on 1 July 1915 while flying his M.5K/MG, but as the victory occurred in the airspace behind Allied lines, over the Forêt de Parroy near Luneville, this could not be confirmed at the time. A similar victory over another Morane "Parasol" two-seater, again unconfirmed, was scored by Wintgens three days later. On the 15th, Wintgens scored his first confirmed victory over a third Morane Parasol, the earliest known confirmed aerial victory for anyone flying a Fokker E-series monoplane in combat.
The M.5K/MG usually used the Parabellum MG14 machine gun for the synchronized armament, which could prove to be a troublesome arrangement, and the five M.5K/MGs built by the Fokker factory in Schwerin/Gorries retained the "shoulder-wing" position of the M.5k for the monoplane wing. Parschau's E.1/15 later had its wing lowered to the "mid-wing" position of the production E.Is, while the remaining four were not known to have been changed. Oswald Boelcke, future German aerial tactician, was issued the third production M.5K/MG, which he flew during July 1915 with Feldflieger Abteiling 62, based near Douai and shared flying time with Max Immelmann After Boelcke achieved his own first aerial victory on July 4 with an Albatros C.I armed two-seat observation aircraft, Boelcke would score his first single-seater victory with E.3/15, over a B.E.2c British two-seater near Arras on 19 August 1915. Immelmann would very soon receive his own lMG 08-armed E.I, serialed E.13/15 for his own use.
E.Is were mainly flown by regular pilots of the Fliegertruppen des deutschen Kaiserreiches, with one Eindecker attached to each six-aircraft Feldflieger Abteilung aerial observation/reconnaissance unit. The first step towards specialist fighter-only aviation units within the German military was the establishment of the so-called Kampfeinsitzer Kommando (single-seat battle unit, abbreviated as "KEK") formations by Inspektor-Major Friedrich Stempel in February 1916, as the E.Is started to leave front-line service.
Following the era of the "KEK" units through the summer of 1916, the Fliegertruppen forces were renamed the Luftstreitkräfte in October 1916, with both units directly serving the German Army; the formation of specialised Jastas (fighter squadrons) in the German air service was still to come. Two E.Is were supplied to the Austro-Hungarian air force and five to the Kaiserliche Marine in April 1916. The E.I was soon joined by the improved Fokker E.II and, as the first E.Is were entering service in June 1915, the first of the E.II type was being demonstrated by Anthony Fokker. Nevertheless E.I production continued in parallel with the E.II, depending on the availability of the Oberursel engines. By 1916, a total of 54 had been manufactured and delivered to the German Army, Navy and the Austro-Hungarian army.