Ksenija's stepmother, Sofija Kondić, who taught at the Women's College (Viša ženska škola) in Belgrade, became her rightful guardian.

An excellent student, she decided to pursue an academic career in philosophy and soon after graduation, began working on a doctoral thesis on Giordano Bruno's De triplici minimo.

She went to Geneva and Paris to seek out rare philosophical works and to discuss her thesis with specialists in the field, and on January 20, 1922, defended her Ph.D with honors in Belgrade before a panel of academics, including rector Jovan Cvijić, Mihailo Petrović, Milutin Milanković, Veselin Čajkanović, and Branislav Petronijević, her mentor.

At a public meeting where many people spoke in support of her, the most prominent speakers were law professor Živojin M. Perić and poets Rastko Petrović and Sima Pandurović.

Pandurović, who stood by her throughout the ordeal, was quoted in a newspaper article saying: "She has been accused at the plenum of the University Council of plagiarism by one member of the faculty who has not the remotest inkling of philosophy and who has unaccountably taken it on himself to defend that discipline from a genuine thinker."

Despite the support Atanasijević received, however, her position at the university was never restored to her, and she spent the rest of her working life—until 1941—as an inspector for the Ministry of Education.

Ksenija Atansijević left a substantial volume of work, including more than 400 texts, among them books and essays in philosophy, psychology, history, and literature.