Eissen is located at the northern border of the Warburger Börde at a gently inclined place.
To the northwest lies Peckelsheim, to the north Schweckhausen, Willegassen and Schönthal, to the east Borgentreich, to the southeast Lütgeneder, to the south Großender, to the southwest Engar and Deppenhöfen and to the west Löwen.