Ms von der Leyen, the European Commission president, said she feels it may not be “feasible” for plans to be finalised by the end of next year.
Her comments come with Britain set to leave the bloc on January 31, after Boris Johnson secured a majority in Parliament, allowing him to move forward with his “get Brexit done” plans.
Negotiations between the remaining EU members and the British government on post-Brexit trade, fisheries, education and transport relations can only begin after that date.
And at present they must conclude by the end of 2020.
“I am very concerned about how little time we have,” Ms von der Leyen told the French business newspaper Les Echos.
“It seems to me that, on both sides, we should seriously consider whether the negotiations are feasible in such a short time.
“I think it would be reasonable to take stock in the middle of the year and if necessary, agree on an extension to the transition period.”
As the leader of the executive commission, she heads the EU institution responsible for Brexit talks and negotiating trade deals on behalf of member countries.
Prime minister Boris Johnson has insisted he wants no more delays to the process, though that leaves Britain and the EU facing a “no deal” scenario at the start of 2021.
Yesterday, the European Commission’s vice president wrote a”love letter” to Britain, in which he said it would always be welcomed back to the EU fold.
Frans Timmermans, a former Dutch foreign minister, said his love for the UK was fostered while studying in a British international school in Rome.
However, he said he now feels like a spurned “old lover” over the split.
He wrote in the Guardian: “You have decided to leave. It breaks my heart, but I respect that decision. You were in two minds about it, like you have always been in two minds about the EU. I wish you had stuck to that attitude, it served you well and it kept all of us in better shape.
“Was it necessary to force the issue? Not at all. But you did. And the sad thing is, I see it is hurting you. Because the two minds will still be there, even after you have left. In the process so much unnecessary damage has been done to you, and all of us. And I fear more will follow.
“But at the same time I find comfort in the thought that family ties can never really be severed. We’re not going away and you will always be welcome to come back.”