On 17 October 1898, Humphrey matriculated for chemistry at the University of Zurich. She joined a growing band of Alfred Werners students, working in the inadequate cellars known as the "Katakomben" (catacombs). Humphrey was awarded a grant of £60 a year for three years by the Technical Education Board of the London County Council, but studying in Switzerland was expensive, and Humphrey was "hard up". Werner recognised Humphreys ability and appointed her as his assistant, with a salary, the first woman to occupy the post. Humphrey worked hard, and her account of the time suggests that she found the social life disappointing.
Humphrey was "the first of his students to succeed in preparing Werners first new series of geometrically isomeric cobalt complexes, a class of compounds that were crucial in his development and proof of his coordination theory." One of these compounds, the cis-bis(ethylenediamine)dinitrocobalt(III) bromide, was the first synthesis of a chiral octahedral cobalt complex. In 1991, the Swiss Committee on Chemistry donated Humphreys chiral crystals to the Royal Society of Chemistry, and they are now at Burlington House, in London.
"What a pity for Miss Humphrey that it was not recognized at the time, because she would then have been responsible for an unequivocal proof of the soundness of Werners coordination theory and the subsequent award of the Nobel prize to him." While one later study has cast doubt on the quality of the sample, Humphreys status as a pioneer woman scientist remains significant.
Her doctoral thesis Über die Bindungsstelle der Metalle in ihren Verbindungen und über Dinitritoäthylendiaminkobaltisalze was accepted by the University of Zurich in 1901. Humphrey was the first British woman to obtain a doctorate in chemistry, though not the first in Zurich. An American chemist, Rachel Holloway Lloyd, had already done so in 1887, and it had become "a haven for women students from all over Europe".
On completion of her thesis, Humphrey was recommended to move to Leipzig University to continue research under Wilhelm Ostwald. However, the attitude to women there was quite different from Zurich, and she would not tolerate a regime where she was not allowed to work in the laboratories in case her presence distracted the men from their work.