Barack Obama and Angela Merkel both agree that strong ties between US and Germany remain vital.
The White House said the pair talked by telephone and agreed cooperation is "essential to ensuring a sturdy trans-Atlantic bond, a rules-based international order, and the defense of values that have done so much to advance human progress in our countries and around the world."
This came after Trump unleashed a volley of attacks on Europe and Merkel in a hard-hitting interview with two European newspapers on Sunday.
The Republican, who takes office Friday, criticized Merkel's "catastrophic" decision to open Germany's borders to hundreds of thousands of refugees and migrants.
He branded NATO "obsolete" and said more countries would leave the European Union after Britain.
The comments were widely condemned on both sides of the Atlantic.
Trump aides have since tried to walk his comments back, insisting he wants a "great relationship" with the German leader.