After talks in the northern town of Hanover where tens of thousands marched yesterday against the planned deal, Obama said the world's largest trade pact could be finalised by the end of the year.
"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.
"I don't anticipate that we will be able to have completed ratification of a deal by the end of the year, but I do anticipate that we can have completed the agreement."
"As you see other markets like China beginning to develop and Asia beginning to develop and Africa growing fast, we have to make sure our businesses can compete."
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Merkel echoed that sentiment, saying the deal was "extremely helpful to allow our economy in Europe to grow".
"It is good for the German economy, it is good for the European economy," she said.
But Obama acknowledged there was popular opposition.
"People are unsettled by globalisation," he said. "People visibly see a plant moving and jobs lost and the narrative develops that this is weakening rather than strengthening the position of ordinary people and ordinary workers."
Ahead of the meeting there was a sign of the significant hurdles that remain.
Merkel's Economy Minister Sigmar Gabriel warned the deal "will fail" if the United States refused to make concessions in "buy American" clauses.