While the persistent rain will clear during the day, the remaining scattered showers will be thundery downpours - with the possibility of 10-15mm of rain within an hour.
According to the Met Office, the south and east of the region are likely to be worst affected and surface water flooding may cause problems on the roads.
"The showers will be slow-moving with a risk of isolated large rainfall totals in a relatively short time," forecasters say.
A yellow warning has been issue for Northern Ireland on Thursday by the Met Office.
P&O Ferries have confirmed that their fast craft sailings from Larne to Cairnryan at 12.55pm on Thursday and from Cairnryan to Larne at 3pm have been cancelled due to the adverse weather.
The company say all booked passengers will be accommodated on the next available conventional sailings, which are operating to schedule.
Forecasters say the rain should ease later in the evening, although more showers will continue into the weekend and even the start of next week.