The weather advisory, which came into effect from midday today, will remain in place until Saturday at 6pm.
Met Éireann has stated that windy weather on Thursday and Friday "may result in unsafe conditions over high ground, lakes and sea areas".
The weather advisory follows a yellow rainfall warning which was issued for Cork and 13 other counties this morning.
The national weather forecaster says heavy and thundery rain can be expected for the duration of today with localised flooding and accumulations of 25 to 40mm in places.
The current "unseasonably wet" conditions have caused significant damage to many roads in West Cork.
Cork County Council has urged motorists to drive with caution.
The Rosscarbery/Glandore Rd (R597) remains closed following flooding.