Skipitis returned to Lithuania in May 1918 and took up teaching in Šiauliai. However, by the end of the year he became a judge in the newly formed Lithuanian judiciary system first in Šiauliai and, when the city was captured by the Soviets during the Lithuanian–Soviet War, in Kaunas. From 6 March 1919 to becoming Minister of the Interior in June 1920, he worked as a public prosecutor. Once, when due to financial difficulties, the Lithuanian government did not pay wages to court officials, Skipitis personally borrowed 12,000 German Papiermarks to pay the wages. He was active in organizing the Lithuanian Riflemen's Union which sent him to Šiauliai in November 1919 to organize the partisan staff for combat with the West Russian Volunteer Army (Bermontians) during the Lithuanian Wars of Independence.