In 1932 he became an employee and in 1947 a deputy head of the newly begun excavations at the Agora of Athens under Homer A. Thompson, a position he held until 1967.
He spent his captivity in Laufen, Germany, where an internment camp was set up in the castle for some American civilians who were unable to leave Europe quickly enough due to the United States' entry into the war.
During this time, he gave lectures on ancient Greek history as part of educational events organized by the prisoners themselves, which he based on a copy of Thucydides that was in his pocket when he was arrested.
As part of a prisoner swap, Vanderpool was released in 1944 and went to Princeton, New Jersey to the Institute for Advanced Study, where he conducted research until 1946.
In particular, his research provided identification (that should be taken with some caution) of a building remnants southwest of the Agora as the state prison in which Socrates was imprisoned before his death.