The rain and thunder, which is moving towards the country from the North Sea, will bring localised downpours during the day, according to a forecast by the Danish Meteorological Institute (DMI).
DMI has issued a storm warning for Thursday and says that up to 25-35mm of rain could fall in some areas.
“The bad weather will hit Denmark within the next few hours and we are expecting thunder in some places. We can not rule out localised downpours,” duty meteorologist Steen Rasmussen of DMI told Politiken.
The storm is expected to reach the southwestern part of the country first before moving east, with heavy rain and thunder probable in southern and central Jutland along with the islands of Funen, Lolland and Falster.
Southern Jutland and Funen are expected to be worst hit.
“The northern part of the country will not escape the rain, but looks likely to avoid the heavy rain on this occasion,” Rasmussen said.
The meteorologist said that there was some risk of flooding in low-lying areas and advised caution during the storm.
“Take cover during thunder, and if you are driving then be careful, as there is a risk of aquaplaning. There may also be strong gusts of wind, so it is important to be aware of this,” he said.
The bad weather is associated with a low pressure area and associated weather front, according to the report.
Danes looking forward to next week's Roskilde Festival – the largest music festival in northern Europe – will see the storms as an unwanted arrival after a period of sunny weather.
The yearly festival, which opens the gates to its 90,000 square metre camping area on Saturday, has around 130,000 attendees – making it Denmark's 4th biggest town for its one-week duration.
Bad weather has in the past turned the festival area into a quagmire, most notoriously in 2007, when 85mm of rain caused flooding and health hazards.
DMI currently forecasts showers and mixed weather in the Roskilde area next week.