Gentleman's Agreement delves into the imperfections of society, specifically the prejudices of the American mainstream in the 1940s. Keenly aware of subtle forms of discrimination, she describes the latent anti-Semitism rampant in America. Hobson focuses on people who do not regard themselves as anti-Semites, and who deny charges of bigotry with the familiar rationalization that "Some of my best friends are Jews." Hobson attempts to show that many of these people are enemies of the Jews as much as are overt anti-Semites.

Social problems are highlighted as Phil Green pursues his reporter's assignment posing as a Jew. Green discovers that Jews are barred admission to various country clubs and hotel resorts as well as prohibited from buying homes in some neighborhoods. He learns the extent to which there is a "gentlemen's agreement" existing in the United States concerning how to treat Jews.

The major theme in Gentleman's Agreement is the need to recognize dominant prejudices and to create a society where people are accepted for what they really are. The story appeals for mutual respect and tolerance for all people. Hobson emphasizes that prejudices are not natural, but learned: "We are born in innocence ... in an unstained purity of heart."