The return leg will take place in Lissywollen next Wednesday.
Athlone Town will face a major uphill battle next week to keep their UEFA Women's Europa Cup hopes alive.
The Women's Premier Division leaders were beaten 3-0 away to Glasgow City in the first leg of their first qualifying round encounter.
Goals from Amy Anderson, Linda Motlhalo and Lisa Forrest has given the Scottish side the advantage ahead of next week's second leg clash.
It comes just days after Colin Fortune's shock resignation as manager.
The return leg is down for next Wednesday at Lissywollen.
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