The Belgian monarch will later go to the capital's Antakalnis Cemetery to lay a wreath at the monument to those who died in the struggle for Lithuania's Independence.
On Tuesday, King Philippe, together with Nauseda, will attend a Lithuanian-Belgian business forum before visiting the Sunrise Valley Science and Technology Park.
The royal couple and the president and his wife, Diana Nausediene, will visit the Old Town of Vilnius and meet with students at Vilnius University.
On Wednesday, King Philippe and Nauseda are scheduled to visit Belgian troops at the Pabrade training area close to Vilnius.
The royal couple and the president and his wife are also scheduled to go to Kaunas, the 2022 European Capital of Culture, to see the city's Art Deco architectural heritage and visit the M. K. Ciurlionis National Museum of Art.
Queen Mathilde will focus on culture and social issues during her visit.
On Monday, the queen and Nausediene are to visit the Vilna Gaon State Jewish Museum.
On Wednesday, they are scheduled to meet with Ukrainian war refugees at a Ukrainian center in Vilnius, and to visit Pirmas Blynas, a restaurant in the Lithuanian capital that hires people with disabilities to help them integrate into society.
The monarchs will be presented with the Order of Vytautas the Great for their personal contribution to the development of relations between Lithuania and Belgium as well as political, economic and societal cooperation between the two countries.