Forecasters say that isolated thunderstorms are expected to travel north across England and Wales early on Thursday morning with as much 50mm of rain possibly falling in three hours.
The intense downpours also bring a low risk of floods and transport disruption with lighting and hail potentially adding more hazards.
A Met Office spokesman said: "Isolated thunderstorms are likely to develop across parts of England and Wales from Thursday morning.
"While these storms may miss many places, where they do develop intense downpours are likely, bringing a low risk of sudden flooding of roads, transport routes, homes and businesses. Lightning and hail may be additional hazards.
"25-30 mm of rain may fall within an hour, perhaps 50 mm in three hours, however such totals are likely to be very isolated, with many places staying dry.
"Some intense showers and thunderstorms may continue overnight into Friday morning before clearing into the North Sea."
The weather warning is in place from 6am on Thursday July 6 to 6am on Friday July 7.