Twenty-seven people died in floods and landslides that washed away roads, railway tracks and bridges, cutting off many populated areas in central and southern Bosnia.
Most of the victims were from a village in the area of the town of Jablanica, about 70 kilometres (43 miles) southwest of Sarajevo.
The village of Donja Jablanica, whose 19 residents were killed, was virtually buried under mud, rocks and granite debris from a nearby quarry.
Von der Leyen visited the village on Thursday during her tour of six Balkan nations.
Accompanied by Prime Minister Borjana Kristo, she talked to mountain rescue service members and heads of several affected municipalities.
"Europe stands with you," she said during the visit.
"And we are here not only for the short run, but also for the mid and long term to help you.
"First of all, of course, to help immediately, but secondly, to reconstruct and rebuild after the disaster," von der Leye added.
"You are friends and partners. You are a candidate country to the European Union."
Local media estimate the damage in five municipalities, excluding destroyed road and railway infrastructure, at least 89.5 million euros ($96.8 million).
Amina Imamovic from Donja Jablanica lost nine family members in the disaster.
She was with her parents in their house during the night when a torrent swept away all nearby houses where her relatives lived and who were all killed.
"Practically half of the village was razed to the ground ... We were saved by the trees that were leaning against the house", the 20-year-old student told AFP.
Von der Leyen started her Balkan tour on Wednesday in Albania where she pledged that membership expansion would be high on the Brussels agenda.
Discussions around EU enlargement in the Balkan region of almost 18 million people stretch back 20 years, with Brussels blowing hot and cold during that period.
The six countries -- Albania, Bosnia and Herzegovina, Kosovo, Montenegro, North Macedonia and Serbia -- are in different stages on their path towards membership in the bloc.
On Friday, EU chief will meet Bosnia's top officials before heading to Serbia.
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