The warning is in place between noon and 11.59pm.
According to the service the areas expected to be impacted in NI are Counties Down and Armagh.
The Met Office say that the public should expect: “spray and flooding on roads probably making journey times longer;
bus and train services probably affected with journey times taking longer; and flooding of a few homes and businesses possible.
They add: “Spells of heavy rain will affect southwest Scotland and parts of Northern Ireland on Wednesday, especially during the afternoon and evening.
“20-30mm is likely quite widely with as much as 40-50mm in a few places, mainly hilly parts of Dumfries and Galloway and South Down.
“The rain will clear away southeastwards later on Wednesday evening”.