Rand indicated that the primary theme of The Fountainhead was "individualism versus collectivism, not in politics but within a man's soul". Philosopher Douglas Den Uyl identified the individualism presented in the novel as being specifically of an American kind, portrayed in the context of that country's society and institutions. Apart from scenes such as Roark's courtroom defense of the American concept of individual rights, she avoided direct discussion of political issues. As historian James Baker described it, "The Fountainhead hardly mentions politics or economics, despite the fact that it was born in the 1930s. Nor does it deal with world affairs, although it was written during World War II. It is about one man against the system, and it does not permit other matters to intrude." Early drafts of the novel included more explicit political references, but Rand removed them from the finished text.
Rand chose the profession of architecture as the background for her novel, although she knew nothing about the field beforehand. As a field that combines art, technology, and business, it allowed her to illustrate her primary themes in multiple areas. Rand later wrote that architects provide "both art and a basic need of men's survival". In a speech to a chapter of the American Institute of Architects, Rand drew a connection between architecture and individualism, saying time periods that had improvements in architecture were also those that had more freedom for the individual.
Roark's modernist approach to architecture is contrasted with that of most of the other architects in the novel. In the opening chapter, the dean of his architecture school tells Roark that the best architecture must copy the past rather than innovate or improve. Roark repeatedly loses jobs with architectural firms and commissions from clients because he is unwilling to copy conventional architectural styles. In contrast, Keating's mimicry of convention brings him top honors in school and an immediate job offer. The same conflict between innovation and tradition is reflected in the career of Roark's mentor, Henry Cameron.
Den Uyl calls The Fountainhead a "philosophical novel", meaning that it addresses philosophical ideas and offers a specific philosophical viewpoint about those ideas. In the years following the publication of The Fountainhead, Rand developed a philosophical system that she called Objectivism. The Fountainhead does not contain this explicit philosophy, and Rand did not write the novel primarily to convey philosophical ideas. Nonetheless, Rand included three excerpts from the novel in For the New Intellectual, a 1961 collection of her writings that she described as an outline of Objectivism. Peikoff used many quotes and examples from The Fountainhead in his 1991 book on Rand's philosophy, Objectivism: The Philosophy of Ayn Rand.