When the VFA went into recess, Atkinson crossed to the Carlton Football Club on a wartime permit, and played there for three years from 1942 until 1944, stepping up as club interim captain in 1944.
During the VFA's recess, Atkinson made the move to the Carlton Football Club under wartime exemptions, playing for the team from 1942 to 1944 and eventually taking on the role of interim captain in 1944.