Due to an illness, Magill received only a third rank in her 1881 tripos honors examinations at Newnham College, which negatively impacted her academic career.

[6][7] Magill's dissertation, The Greek Drama, was long considered lost, but in 2018 it was found in her papers in the Rare Book and Manuscript Collections, Cornell University Library.

[8][9] After serving as the principal for a year at a private school in Johnstown, Pennsylvania, Magill was selected on the recommendation of Edward Everett Hale to organize Howard Collegiate Institute[10] in West Bridgewater, Massachusetts in 1883.

Howard was a non-sectarian school for about forty women and Magill had the authority to choose teachers and conduct college courses.

Helen Magill met Andrew D. White in 1887 while she was presenting a paper about her time at Newnham College at the American Social Science Association.

"[11]White encouraged Magill to apply for the post of Director of Sage College for Women at Cornell University.

While teaching at Brooklyn High School, Magill maintained a correspondence with White where she commented on her perceived failings:"but it makes me miserable sometimes to think what I might have already done, if I had produced more and criticized less."

Magill was presented at both courts and was a noted conversationalist, discussing architecture, sculpture, music, and literature with Kaisar Wilhelm II.