His doctoral thesis was directed by Karl Dietrich Bracher and examined US-foreign policy "between idealism and realism".
In 1980/81, he was a graduate student associate at the Harvard Center for International Affairs (CFIA) under the auspices of Samuel Huntington.
From 1977 to 1985, Pflüger was also a member of the federal executive committee of the Young Union (JU), the youth organization of the CDU/CSU, under the leadership of successive chairmen Matthias Wissmann and Christoph Böhr.
Between 1989 and 1991, Pflüger worked as manager of the Matuschka Group, Berlin, at that time a leading German investment bank.
In November 2005, he was appointed Parliamentary State Secretary at the Federal Ministry of Defence under minister Franz Josef Jung, a position in which he remained until October 2006.
During his time in office, he managed to negotiate the continuing cooperation with President Karimov and the Uzbek government to use the Termez airbase by the German armed forces in December 2005.
After spending almost no time preparing his election campaign, he lost to incumbent Klaus Wowereit of the SPD, as all the polls had indicated.
Pflüger was an outspoken advocate of opening the CDU for a possible coalition with the Free Democrats (FDP) and the Greens (a so-called "Jamaica"-coalition).
In 2010, Pflüger announced his decision to withdraw from his political functions and to focus on his role as the Director of the European Centre for Energy and Resource Security (EUCERS), King's College London.