Chelsea loanee Gabriel Slonina conceded a 93rd minute equaliser to his opposite number, Tom Vandenberghe, as the shot-stopper scored a dramatic late goal.
Iceland international Victor Pálsson fired Eupen ahead in the 69th minute and the Belgian side thought that they had sealed the victory.
However, it was not to be as the most unlikely of goalscorers pulled Kortrijk level in the dying moments.
With just three minutes of added time, the goalkeeper made his way up for an attacking corner and got his head onto the cross to knock the ball down towards goal.
Unfortunately for Chelsea loanee Slonina, he could not prevent the ball going in despite getting a hand to the header as Vandenberghe ran off celebrating with his team-mates.
Goalkeeper Tom Vandenberghe scored an incredible 93rd-minute equaliser this weekend
The shot-stopper rose highest to head past Chelsea loanee Gabriel Slonina in the Eupen net
The goal was the last action of the game, with Slonina and Co. having to pick their heads up and go again.
While the defending from the corner was poor, 19-year-old Slonina will no doubt think that he could have done better.
He embarked on his second loan move since arriving at Stamford Bridge this summer as he joined Eupen.
The youngster initially returned to Chicago Fire to complete the MLS season after the Blues finalised his signing.
Chelsea will have high hopes for the shot-stopper, fighting off interestest from Real Madrid to secure his signature.
Perhaps he will live up to his potential and become the Blues' first choice once day, with Robert Sanchez occupying that spot currently.
Kortrijk will be hoping that Vandernberghe's strike can prove to be a boost for them as they sit bottom of the Belgian Pro League.
Eupen, their relegation rivals, are now winless in four and will be looking to recover this season.