Rebane served as an officer in the Estonian Army until Soviet troops occupied the country in 1940. The Soviets disbanded and absorbed most of the Estonian Armed Forces and arrested and executed the entire Estonian high command. Many junior officers, such as Rebane, were dismissed due to their lack of "political reliability" and were liable to be deported. For a while, Rebane worked in construction, then fled into the forests when the Soviets began mass deportations in 1941. He established and led an anti-Soviet Forest Brothers unit in Virumaa (Northern Estonia) in May 1941.