An agreement between the government and LFF is planned to be signed during the meeting to promote cooperation in strengthening football in the country.
Ceferin, who is coming to Vilnius at the invitation of LFF President Tomas Danilevičius, will be present at the signing ceremony.
Skvernelis mentioned last week that Ceferin and he would discuss, among other things, the issue of a national stadium in Lithuania.
After certain legal hurdles have been cleared, Vilnius' local authority continues talks on the construction of a national stadium in the capital with Axis Industries, an engineering product and solutions company owned by Icor, and its partners.
The consortium offers to build the complex for 79.9 million euros.
Ceferin is also scheduled to meet with LFF's top officials during his visit.
Michel Platini was the last UEFA president to visit Lithuania back in 2011.