"I want to thank you and your country for being a brilliant host nation. We found everything prepared for the German troops," she told reporters in Vilnius.
During her visit, von der Layen is meeting Lithuanian President Dalia Grybauskaitė and Defence Minister Juozas Olekas.
Von der Leyen is also to participate in a meeting of the leadership of the European People's Party group, the largest political group in the European Parliament, in Vilnius.
Vilnius and Berlin have stepped up defence cooperation following Russia's actions in Ukraine. Diplomatic ties between the countries have intensified and Lithuania has been purchasing military equipment from Germany.
The German-led NATO battalion is planned to be deployed to Lithuania next spring.