The Danish club were formed in a merger in 1999, gradually improving over the last decade, and they are now challenging the dominance of Danish powerhouses FC Copenhagen and Brondby.
The first leg will be played at Eastlands on August 14 with the return leg on August 28.
The away leg will be a step up from the first qualifying round in the Faroe Islands as Midtjylland play at a 12,000-seater stadium in Herning.