The Macedonians finished fourth in their domestic league last season, a full 40 points behind runaway champions Shkendija.
Managed by Zekirija Ramadani, a former defender, they will be looking to emulate Progres Niederkorn, who knocked out the Glasgow team at the same stage last season.
The first leg will mark Shkupi's first ever foray into European competition.
They play league matches in the 6,000 capacity Cair stadium, which is situated in the Macedonian capital, Skopje.
However it has yet to be confirmed where the second leg will take place, as all three Macedonian sides in the competition - including FK Vardar, and FK Rabotnicki - are all based in Skopje.
In 2012, the club - now named FK Sloga Jugomagnat - were merged with FC Albarsa to form the existing FC Shkupi, however the national football federation does not legally class them as successors to Sloga.
Much like Rangers, Shkupi are on a pre-season break and haven't played a competitive game since May, when they beat FK Vardar 4-1 at home.
The last Scottish side to face Macedonian opposition were Aberdeen, who progressed past Shkendija on away goals in 2015, after a 1-1 draw in Skopje was followed by a goalless stalemate at Pittodrie.
By Andy Harrow