The talks will focus on "German support for Ukraine and efforts to secure a ceasefire" with Russia to end more than three years of war, German government spokesman Stefan Kornelius said.
A member of Zelensky's delegation confirmed to AFP that they had arrived in Berlin ahead of the talks with Merz scheduled for noon.
The two leaders are also expected to discuss EU efforts to levy more sanctions on Moscow amid a lack of progress so far towards a ceasefire and eventual peace talks.
After a joint press conference with Merz and talks with German business leaders, Zelensky is due to meet German President Frank-Walter Steinmeier at Bellevue Palace.
The Berlin visit comes days after Russia launched some of its heaviest missile and drone attacks of the conflict on Ukraine, and as US President Donald Trump has voiced growing frustration with Russia's President Vladimir Putin.
Conservative Merz, who took office on May 6th, has vowed to continue strong backing for Ukraine in concert with Paris, London and Warsaw.
He has also pushed to ramp up German defence spending with the goal of creating Europe's "strongest conventional army", a plan Russian Foreign Minister Sergei Lavrov on Wednesday branded "very worrying".
Taking over from centre-left leader Olaf Scholz, Merz has changed the tone in Berlin and voiced harsh criticism of Putin who, the chancellor charged this week, "obviously sees offers of talks as a sign of weakness".
Scholz had also strongly backed Kyiv but shied away from sending it long-range Taurus missiles, worried that this might escalate tensions with Russia.
Merz has in the past said he favours delivery of Taurus, but his new government has stressed it would no longer detail what arms it sends to Ukraine, preferring a stance of strategic ambiguity.
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Sanctions pressure grows
Russia's full-scale invasion of Ukraine, launched in February 2022, has resulted in tens of thousands of deaths and ravaged large parts of the east and south of the country.
Diplomatic efforts to end the fighting had accelerated in recent weeks, with Russian and Ukrainian officials holding direct talks for the first time in three years earlier this month.
But Putin has been accused of stalling peace talks and the Kremlin has shown no signs of scaling back its maximalist demands.
Trump, who has long promised he would broker a quick end to the war, issued a rare rebuke of Putin on social media on Sunday.
"I've always had a very good relationship with Vladimir Putin of Russia, but something has happened to him. He has gone absolutely CRAZY!"
On Tuesday, Trump charged that Putin was "playing with fire", as the Wall Street Journal and CNN both reported that the US president was now considering fresh sanctions as early as this week.
German Foreign Minister Johann Wadephul was due to hold talks in Washington on Wednesday which he said would focus on "our common goals: We want to finally end the deaths in Ukraine, we want an immediate ceasefire and we want a lasting peace."
"In order for Putin to finally come to the negotiating table, for Russia to finally enter into serious negotiations, we must maintain the pressure," Wadephul added, pointing to European efforts to tighten sanctions.
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