Merkel will also travel to Rukla to visit troops of the German-led NATO multinational battalion, which has been stationed in the central Lithuanian town since last year.
The chancellor's visit, scheduled for next Friday, reflects strong relations between Lithuania and Germany, the office said.
Grybauskaitė and Merkel will discuss the key issues on the EU's agenda, defense cooperation and economic relations, it said.
The German and Lithuanian leaders will discuss the EU's response to migration challenges, the Brexit process and the bloc's new multiannual budget.
Germany is one of Lithuania's key partners for military acquisitions. Lithuania buys German-made Boxer infantry fighting vehicles, self-propelled howitzers, armored vehicles, naval and machine guns, and grenade launchers.
Germany is also the third-largest foreign investor in Lithuania. Germany's car parts giant Continental last summer launched the construction of a new 95-million-euro factory in the Kaunas free economic area, marking the biggest investment in Lithuania's manufacturing sector in 20 years.
This will be Merkel's third visit to Lithuania.