The Met Office announced the warning in southern and eastern Scotland between midnight and 10am on Tuesday.
Rain, which the forecaster said would be “heavy at times”, could lead to travel disruption.
The news comes as a thunderstorm warning covered most of Scotland on Monday, with the Met Office saying a “large” storm was moving north east in the morning.
The weather follows an extended dry period, which has seen temperatures consistently rise above 20C in the past week north of the border.
Meanwhile, thunderstorm warnings will be in force in some parts of England until Wednesday.
The country in its entirety will be under threat of thunder on Tuesday while the South could see more storms until the end of Wednesday.