The warning comes into force at 10am on Thursday, September 9 and will remain in place until 8pm.
It covers the whole of mainland Scotland and reaches as far west as Stornoway.
Forecasters have also warned that some areas may experience flooding as a result of the heavy showers and thunderstorms.
The Met Office has said there is a small chance that homes and businesses could flood and face damage from lightning strikes, hail or strong winds.
Travel disruption may follow the bad weather with a chance of delays and cancellations.
Drivers are urged to travel with caution as spray and sudden flooding can make for dangerous conditions.
A statement on the Met Office website says: “A further yellow weather warning for thunderstorms has been issued on Thursday.
"Once again, it's important to note there is a very low likelihood that any one location within the area will experience impacts from thunderstorms, but where the storms do occur up to 30mm of rain is possible in less than an hour which has the potential to generate some surface water flooding.
"There is also the possibility of very localised impacts from lightning and hail.”
The warning comes after the news that temperatures in some parts of Scotland on Wednesday could reach the highest on record for a September day in over 100 years.
Met Office meteorologist Marco Petagna said if a temperature of more than 28.1C is recorded it would be Scotland’s hottest September day since 1906.