Niels Bohr entered the University of Copenhagen in 1903. While he took advantage of the school's science offerings, perhaps one of the most important single courses he took was a philosophy class with Professor Höffding, who had been his father's close friend. Höffding was among the colleagues whose visits had contributed essentially to Bohr's early intellectual development. Höffding surveyed the key philosophical systems from the sixteenth to eighteenth century, placing the emphasis on central questions rather than on any one theory. Bohr became so engaged with some of these questions that he considered turning to epistemology at one point. Although he would later return to epistemology as it related to his work quantum mechanics, his interest in philosophy began independent of the scientific context and may have influenced his work in physics as much as the reverse case.

Bohr encountered another major influence on his development when he and Harald were invited to join a discussion group of students from Höffding's course. Debating primarily philosophical questions raised in Höffding's course, the group, dubbed Ekliptika and limited to twelve members, featured future jurists, historians, psychologists, entomologists, and etymologists. Both Niels and Harald were active members of the debate, and one member, Vilhelm Slomann the art-historian, recalls that their thinking was so closely integrated that they often expanded on each other's thoughts spontaneously in an awe-inspiring intellectual partnership. This method of refining ideas became characteristic of Bohr's process. He preferred conversation to working alone, and he felt most productive when he had successfully established a harmonious connection and a comfortable environment.

Despite these additional and related interests, physics remained the passion of Bohr's life. His undergraduate career culminated in a prize-winning project on the surface tension of liquids, offered by the Academy of Sciences and Letters. Working from the theoretical projections of Lord Rayleigh, Bohr sought a way to measure surface tension with the use of vibrating water jets. The experiments seemed never ending, and Bohr's father had to persuade him to stop and actually write the paper. Bohr was awarded the academy gold medal, having at the age of twenty-one modified and expanded upon the theories of Rayleigh, one of the most famous physicists of that period. Moreover, the significance of this work reappeared many years later when the surface tension of water proved relevant to Bohr's study of the atom (and subsequently to nuclear energy and the atom bomb). No one could have foreseen this development, particularly the Academy, which had chosen the topic only because most physicists were unfamiliar with it. This coincidence illustrates the unity of Bohr's career, as he rarely touched on tangents that would not somehow fit into his larger projects.

Bohr moved directly into research for his master's thesis. Again he found it hard to recognize when to conclude, and his brother, who had begun his research later, actually completed his thesis and examinations first, going on to study with the German mathematician Edmond Landau. Bohr could not have been more proud of his brother's achievements, but he soon found reason to celebrate his own: his gold medal paper was published in Philosophical Transactions, a distinguished English journal. Soon Bohr completed his doctorate, which he received in 1911 for his work on the electron theory of metals. Like much of his early work, this research foreshadowed issues that he explored and transformed later in his career. His doctoral research, while fruitful, began pointing him to limitations in classical physics with regard to electron behavior, indicating the need for fundamental changes beyond the standard revising that had been going on to this point.

In 1910, shortly after receiving his master's degree, Bohr met Margrethe Nørlund, who became his wife two years later. Her charm and beauty captured his love, and she found his sincerity, modesty, and intelligence alluring. She remained a devoted companion for life, and the two shared over fifty years of happy marriage. They had six children, four of whom survived to adulthood and bore children who delighted their grandparents in their later years. While accounts of Bohr's family life are limited, he achieved personal happiness that complemented his rich professional success.