"Strong and violent storms are expected starting this afternoon until midnight north of the Alps, and in the (southern) Valais and Graubuenden cantons," the Swiss government said in an alert.
It said large parts of the country were under a category 4 warning of "dangerous meteorological incidents of unusual intensity", out of a maximum level of 5.
The government called on the population to stay indoors and to avoid forests, mountain crests, water flows and steep hills.
Storms have already raged this week, with weather forecasters caught off guard on Wednesday as thunderstorms across Switzerland caused extensive local damage.
The country has been sweltering in the grip of a heat wave for several days with temperatures soaring to the mid to high-30s.
But it couldn’t last forever, and despite sunny predictions from MeteoSwiss, the skies darkened with ominous grey-black clouds on Wednesday as gusting winds were followed by violent electrical storms.
Emergency services soon began receiving reports of local damage, with trees uprooted and cellars flooded in parts of the country.
Zofingen in Canton Aargau was particularly affected along with Thun and Langenthal in Canton Bern.
Cantonal police received a large number of reports but said it was not yet possible to estimate the full cost of the damage. The fire brigade said it was stretched beyond capacity in certain areas.
Temperatures are forecast to drop back to a comfortable 23 degrees at the weekend and the beginning of next week – perhaps a welcome relief to the many Swiss suffering from heat stroke.