"Angela and I agree that the United States and the European Union need to keep moving forward with the Transatlantic Trade and Investment Partnership negotiations," Obama said in the northern German city of Hanover after talks with Chancellor Angela Merkel.
"I don't anticipate that we will be able to have completed the ratification of a deal by the end of the year but I do anticipate that we have completed the agreement," he said.
The planned trade pact known as TTIP has run into major opposition, not least in Europe's top economy Germany, where critics have raised the spectre of eroding ecological and labour market standards and condemned secrecy shrouding the talks.
On the eve of Obama's visit to Germany, tens of thousands of people marched through the streets of Hanover against the planned accord.
Merkel's Economy Minister Sigmar Gabriel also cast doubt today on plans to conclude the deal this year, warning the deal "will fail" if the United States refuses to make concessions in the protracted talks.