Bikowsky started her CIA career in the 1990s as a Soviet analyst. She was brought into the Bin Laden Issue Station when it was created in 1996 by its first chief, Michael Scheuer. Sometime after the USS "Cole" bombing in October 2000, she was promoted to Deputy Chief of the Bin Laden Issue Station. By March 2003, she had been appointed Chief of the station. The station was closed in late 2005.