Stranraer were left to rue missed opportunities as a late double earned East Kilbride their second win of the season.
John Robertson had put Kilby in front from the spot after Finn Ecrepont penalised for a foul in the box, but Sallu Turay equalised four minutes after the restart.
With Corey O’Donnell unable to capitalise on a string of second half chances, goals from Rhys Breen and Joao Balde saw EK take all three points.