Ursula von der Leyen said in a video statement that the US and EU were "friends and allies" and said the US presidential election was a "moment of significance also on this side of the Atlantic".
The EU "stands ready to intensify cooperation" with the new US administration, the European Commission president has said.
Von der Leyen congratulated President-elect Joe Biden and Vice President-elect Kamala Harris and said she looked forward to working with them on "pressing global challenges".
Those include the pandemic, climate change, digital regulation and global security, she said.
Many world leaders have been quick to congratulate the incoming administration, with some likely hoping to see new US leadership after the Trump administration's "America First" foreign policy.
Von der Leyen called the US-EU partnership "unprecedented", stating it was rooted in "common history and shared values of democracy, freedom, rule of law, the respect for human rights, social justice, and an open economy."
She was one of a number of European leaders to congratulate the incoming US president, who formerly chaired the Senate's Foreign Affairs committee.
German Chancellor Angela Merkel also congratulated the president-elect, stating that the "transatlantic friendship is indispensable if we are to deal with the major challenges of our time."
Experts have said that Trump's withdrawal from the Paris agreement and contempt for multilateral organisations have impacted the transatlantic partnership.