From 1941 to 1953 (so until Stalin's death), there were 35 mass deportation waves where Lithuanians - mostly landowners, political activists, culture figures and intellectuals - were forcibly removed and sent to remote, barely habitable areas in Siberia and Gulag forced labour camps (like Azeem mentioned already, although that was mainly reserved for guerilla fighters and political prisoners) together with their families. The official numbers, depending on the source, vary from 150.000 to 300.000 people, mostly women and children, so that makes up around 6-12% of the population at the time. In addition to that, around 200.000 ethnic Russians were moved to Lithuania at that time as another part of Sovietization policies.
Around 250.000 people were displaced before the occupation, but that was mostly due to war and impeding annexation.
During the time in the Russian Empire earlier, displacement was not really a thing, and assimilative russification policies such as banning Lithuanian press, schools, religion, cultural events etc. were preferred. I think we are the only nation in the world that has a word for "book smuggler", lol