And she made it clear that, in her view, climate change had played a role in the disaster.
Four Slovenians and two Dutch tourists died in last week's flooding, which also flooded tens of thousands of houses.
"We will make accessible 400 million euros, 100 million of them still this year and 300 million euros next year" from the solidarity fund, von der Leyen told reporters after touring affected areas.
"It was heartbreaking to see the devastation that the rain and the flooding and the mudslides have caused," von der Leyen said.
Slovenia could also request 2.7 billion euros from the EU's "Next Generation" fund, she said.
In addition, 3.3 billion euros of cohesion funds already allocated to the country until 2027 could be repurposed.
Von der Leyen was speaking at a joint news conference with Slovenian Prime Minister Robert Golob.
"Several tens of thousands of houses have been flooded and several thousands of families are in despair today wondering how they will survive the next weeks and months," Golob said.
He urged the EU Commission to release the funds as soon as possible.
Golob has described rains and flooding that hit two-thirds of the Alpine country of two million as its worst natural disaster since independence over three decades ago.
- Climate change blamed -
The flash floods and landslides that began Thursday submerged large swathes of central and northern Slovenia, cutting off access to villages and disrupting traffic.
Clean-up operations are continuing with the help of neighbouring countries.
The government is still assessing the damage, but it says it could come to several billions of euros -- up from an earlier estimate of half a billion.
Streets in the town of Crna na Koroskem -- that were cut off for several days in northern Slovenia -- were still covered in mud on Wednesday. Bulldozers were clearing earth and gravel from the river banks and roads.
"Most likely there will be more situations (natural disasters) like this in the future, and we should prepare," said Golob.
"Certainly in this natural disaster, climate change played a role without any question," said von der Leyen.
The Intergovernmental Panel on Climate Change (IPCC) is unequivocal about the impact of human activity on global warming.
It recently noted that climate change is already affecting many weather and climate extremes in every region across the globe.
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