Russian President Vladimir Putin said many issues had "piled up" between the two countries. The meeting meant Putin had to delay his talks with Japanese Prime Minister Shinzo Abe and the leaders barely made it to the start of a concert held at the Elbphilharmonie concert hall.
It comes at a tense point for the two countries who are at odds over Syria, Ukraine and under a cloud over election meddling. President Trump has said he would like to have a "great relationship" with Russia, however it comes under a cloud of alleged interference in the US election.
The discussion took place behind closed doors, with US Secretary of State Rex Tillerson and Russian Foreign Minister Sergei Lavrov, as well as two translators present.
Before the meeting, Trump said he would look forward to "discussing various things" with Putin.
"We've had some very good talks. We look forward to a lot of very positive things happening for Russia, for the US and for everybody concerned," he said.
"It's an honour to be with you so thank you."
Putin said he was "delighted to meet" the US leader after having spoken on the phone several times.
"Naturally, telephone conversations are never enough if we want to find solutions to pressing issues on the bilateral agenda and the most sensitive, acute issues on the international agenda," he said.
Trump's son Donald Junior took to Twitter to complain about the cameras in the room, as their shutters made it difficult to hear what was said.
"With all the Cameras clicking away rapid fire you can't actually hear what they're saying? How many pictures do you need of the same scene?" he said on Twitter.
The first sit-down meeting between the pair came after a brief encounter earlier in the day when they shook hands behind the scenes.
Footage from the moment shared by German Chancellor Merkel's spokesman Steffen Seibert showed Trump approach Putin and hold out his hand for a shake, while clasping his arm.
A moment later he is also seen patting Putin on the back while European Union leaders Jean-Claude Juncker and Donald Tusk watch on.
The meeting comes during a host of hot-button issues that have made for fractious international relations including the North Korean missile crisis, war in Syria and allegations of Russian interference in the US election.
Earlier in the day the leaders posed for a "family photograph" with President Trump chatting amiably with Australian Prime Minister Malcolm Turnbull while walking into the event.
Once inside the room, where the leaders met to discuss trade and growth strategies, he was seen chatting to German Chancellor Angela Merkel and French President Macron.
The US leader also unwittingly provided a moment of comedy when Merkel suggested the leaders turn for a photograph for the press. Trump, apparently engrossed in his notes, ignored the suggestion leaving him the only one with his back to the media, before turning around and laughing.
Before the meeting, political observers in Washington were worried about the high stakes encounter given Trump's propensity for speaking off the cuff. The last time he met with a Russian official in Washington he was alleged to have disclosed "code word" Israeli intelligence.
He also had to walk a diplomatic tightrope of not wanting to appear soft on Russia while still trying to build a rapport.
But some feared Putin's mastery of international affairs could make Trump a target for manipulation. The former KGB spy has a reputation for strongarming his counterparts, including once bringing his dog to a meeting with German Chancellor Anglea Merkel after having been briefed she was not a fan of the animals.
Pictures from the 2007 meeting show Merkel looking uncomfortable as black labrador Koni appears at Putin's summer house in Sochi.
"I wanted to do something nice for her," Putin said at the time.
"When I found out that she doesn't like dogs, of course I apologised."
Former Ukraine ambassador Steven Pifer said in the lead up to the meeting there was a "fair amount of nervousness" about how it would be managed "because they see a lot of potential risks."
Other leaders are also braced for tough talks with Trump after his "America First" approach to trade and globalisation.
The summit brought together Chinese President Xi Jinping with Trump and Putin amid continued nuclear testing in North Korea, as well as Turkish and Saudi Arabian leaders during the deepening crisis in the Gulf over isolation of Qatar.
