Merkel's spokesperson Steffen Seibert announced on Tuesday that Putin would arrive for the summit alongside President Francois Hollande of France and Petro Poroshenko, the leader of Ukraine.
It will be Putin's first visit to Berlin since Russia annexed the Crimea from Ukraine in 2014, leading to EU sanctions against Moscow.
The summit, at Merkel's invitation, will also "discuss the next steps in the process towards ending the crisis in eastern Ukraine," a statement said Tuesday.
Hollande called on all parties in the Ukraine conflict to draw up a road map to end the crisis, after talks with Poroshenko last Thursday.
The aim would be to help Ukraine regain control of its borders with Russia, he said after speaking by telephone with Poroshenko.
Hollande had spoken last Wednesday with Merkel and Putin about organizing a summit on the conflict.
Russia, which annexed Ukraine's Crimean Peninsula in 2014, backs a separatist, pro-Moscow insurgency in eastern Ukraine that has claimed nearly 10,000 lives.
Moscow has denied accusations that it has sent troops and weaponry across its border with Ukraine to fuel the conflict.
Germany currently holds the rotating presidency of the Organization for Security and Cooperation in Europe (OSCE), which has monitors in eastern Ukraine.
All sides agreed to a peace deal brokered by Germany and France in February 2015, but while the so-called Minsk accords reduced the intensity of fighting, they failed to stop it.
Wednesday's meeting under the so-called "Normandy Format" grouping the four countries will come amid tensions between France and Russia over Moscow's role in the Syrian conflict that prompted Putin to cancel a visit to Paris.