In 1891–1893, he helped combat a cholera outbreak as a result of the Russian famine of 1891–1892. After the graduation, he briefly worked at the clinics of the University of Königsberg before taking up a private practice in Ariogala. He actively supported Lithuanian book smugglers who transported and distributed the banned Lithuanian publications. He was implicated in the large case against Lithuanian activists and book smugglers in 1900 (known as Liudas Vaineikis case) and was sentenced to two years of exile in February 1902. He was exiled to Kazan. He briefly returned to Lithuania in 1904 but was mobilized to serve as a medic in the Russo-Japanese War, including in the Battle of Mukden. He returned to Lithuania and settled in Garliava where he lived until his death. The Lithuanian press ban was lifted in 1904 and Lithuanians were allowed to organize their own cultural societies. Šliūpas became an active organizer. He helped organize and in 1904–1906 chaired the Daina Society which organized concerts and theater performances. He also helped organize the Saulė Society which established Lithuanian-language schools and the Lithuanian Scientific Society which promoted scholarly research, and supported "Ateitis" and "Pavasaris" magazines for Catholic youth. In 1910, together with Saliamonas Banaitis and others he organized the consumers' co-operative Nemunas and was its chairman in 1910–1914.