Merkel's spokesman Steffen Seibert said the meeting would come before the summit, "most probably in the early evening of Thursday".
The pair are also scheduled to talk by telephone today, Trump said in a tweet.
Transatlantic differences on climate change, trade, defence spending and refugees hang over the July 7-8 meeting of the world's major industrialised and emerging economies.
Last week Merkel met with key European leaders and vowed to make a stand for climate protection and open markets at the meeting with Trump, who has said he will take the US out of the Paris climate deal and pursue a protectionist "America First" policy.
Merkel said that "the differences are obvious and it would be dishonest to try to cover that up. That I won't do."
She also said the US exit from the 2015 Paris climate pact had made Europe "more determined than ever" to make the accord a success.
Today, presenting her party's election platform, she predicted "a whole series of thorny issues" at the G20.
"We know the positions of the US government and I do not expect them to disappear on a two-day trip to Hamburg," the chancellor said.
She warned against high expectations, noting that the summit's final communique has to be "approved unanimously".
She said that while there would be common ground on combating terrorism financing, "in other areas there are many differences".
German President Frank-Walter Steinmeier, a former foreign minister, also said current differences with the US are unlikely to end.
"If everyone in the world is looking for the best deal then in the end we all lose," he said in an interview with Stuttgarter Zeitung.
"I am very worried by these changes (in US foreign policy), and we cannot expect quick changes."
More than 20,000 police will be on duty for the G20 meeting, whose participants include China's President Xi Jinping, Russia's Vladimir Putin and Turkey's Recep Tayyip Erdogan.
More than 30 anti-capitalist protests are expected.
A day before the G20 starts, Trump will head to Warsaw for a meeting of central and eastern European leaders likely to include Hungary's hardline Prime Minister Viktor Orban, who has sparred with western European leaders, especially on the refugee issue.