"We are ready to start working with the international community to get the broadest international support possible for this specialised court," von der Leyen said.
Ukraine has been pushing for the creation of a special tribunal to prosecute Russian military and political leaders it holds responsible for starting the war.
The Hague-based International Criminal Court (ICC) launched its own investigation into alleged crimes against humanity and war crimes days after Moscow's Feb. 24 invasion, but it does not have jurisdiction to prosecute aggression in Ukraine.
"While continuing to support the International Criminal Court, we are proposing to set up a specialised court, backed by the United Nations, to investigate and prosecute Russia's crime of aggression," von der Leyen said.
Russia, which calls its actions in Ukraine a "special military operation", has denied targeting civilians.
The G7 agreed on Tuesday to set up a network to coordinate investigations into war crimes as part of a push to prosecute suspected atrocities in Ukraine.
(Reporting by Bart Meijer and Stephanie van den Berg; Editing by Andrew Heavens and Nick Macfie)