At the outbreak of war in September 1939, Thomas McKitterick was an extra-mural lecturer in International Relations, in the University of Wales. When permitted so to do by a change in the schedule of reserved occupations, he enlisted with the Royal Fusiliers in August 1940, and, being a fluent linguist, was in March the next year commissioned Lieutenant in the newly-formed Intelligence Corps. After brief periods of attachment to the Matlock training centre and to MI9 in London, McKitterick was posted to MI12 (Middle East) where, through having listed Greek as his eighth-strongest foreign language, he was appointed a censorship officer in Haifa with particular responsibility for scrutinising the large quantity of Greek correspondence generated in the city. While disliking the posting, and repeatedly requesting a transfer, McKitterick became, almost despite himself, fluent in the language and, increasingly, an expert on the politics of Greece, a nation then still under German occupation.

Eventually, the Army came to make use of these hard-won skills. In January 1944, McKitterick was attached to Cretan Section Force 133 Special Operations Executive (SOE), responsible for the selection of Allied agents to operate on the island. Thereafter, following a spell as an intelligence officer with the Political Information Centre Middle East (PICME) in Cairo, he spent some unhappy weeks at the end of 1944 in liberated Athens, as head of the city section of PIC. Unfortunately, his junior rank and the hostility of British political officers, including Harold Caccia, the future Lord Caccia, made his task impossible, and he was transferred to other intelligence duties.