Von der Leyen told the Frankfurter Allgemeine daily that the pilot programme was focused on training migrants in a variety of areas such as technology, medicine and logistics.
It was not immediately clear if von der Leyen planned to expand the programme to include more of the one million migrants who arrived in Germany last year.
“The idea is that they will go back to Syria one day and help with the reconstruction” of their war-shattered country, von der Leyen told the newspaper.
She said Germany could also play a role in training Syrian security forces once it had a responsible government.
Syrian refugees can carry out civilian tasks for the German military, but are not eligible to work as soldiers, she said.
Von der Leyen sparked controversy within her own Christian Democratic party recently when she suggested that EU citizens could in certain cases take over armed roles in the German military. The defence minister also advocates greater diversity in the German military and moves to recruit more immigrants.