Despite her concerns, Pechey became one of the Edinburgh Seven, the first seven female undergraduate medical students at any British university, others being Mary Anderson, Emily Bovell, Matilda Chaplin, Helen Evans, Sophia Jex-Blake and Isabel Thorne.

She proved her academic ability by achieving the top grade in the chemistry exam in her first year of study, making her eligible to receive a Hope Scholarship.

The four students who achieved the highest marks sitting the first-term examination in chemistry for the first time were to be granted free use of the facilities of the University laboratory during the next term.

Crum Brown, the Professor of Chemistry, was concerned that awarding the scholarship to a woman would provoke a backlash from the male students, who had grown increasingly hostile when they saw that women were capable of outstripping them in competitive examinations.

The Times said: "[Miss Pechey] has done her sex a service, not only by vindicating their intellectual ability in an open competition with men, but still more by the temper and courtesy with which she meets her disappointments.

"[8] The Spectator was satirical: "To make women attend a separate class, for which they have to pay, we believe, much higher fees than usual, and then argue that they are out of the pale of competition because they do so, is, indeed, too like the captious schoolmaster who first sent a boy into the corner and then whipped him for not being in his seat.

She worked for a time at the Birmingham and Midland Hospital for Women, apparently on the strength of her testimonials and successful studies, despite the lack of an official qualification.

[12] For the next six years Pechey practised medicine in Leeds, involving herself in women's health education and lecturing on a number of medical topics, including nursing.

She wrote to Pechey on the idea of working at Bombay (now Mumbai) as Senior Medical Officer (SMO) at the Cama Hospital for Women and Children.

[16] She met Herbert Musgrave Phipson (1849–1936), a reformer, wine merchant and a founding secretary of the Bombay Natural History Society as well as the "medical women for India" fund, marrying him in March 1889.

Five years later, as a result of diabetes and general ill health, she retired from hospital work but continued for some time with her private practice which served the Bombay elite.

In 1896, when bubonic plague struck the city, she played her part in public health measures, and criticisms she made of the way the crisis was handled proved to be influential in managing an outbreak of cholera.

She was at the forefront of the Mud March demonstration organised by the National Union of Women's Suffrage Societies in 1907, but was becoming ill and soon needed treatment for breast cancer.