In 1882, Annie Alexander, age seventeen, entered the Woman’s Medical College in Philadelphia. The Woman’s Hospital Dispensary for Women and Children was located next door to the Medical College. This provided many opportunities for the students to obtain clinical and practical experience. This training was essential if women physicians were to make any achievements in medicine. For many years, hospitals and medical schools in Philadelphia prohibited women from entering the male-dominated facilities. Eventually the Woman’s Medical College solved this problem with the construction of the new building that Annie attended. Inside were laboratories and an operating amphitheater where students could observe surgeries.
The course of studies at the Philadelphia Medical College for Women was rigorous and practical. The majority of the classes prepared the future doctors for a career in Obstetrics. Annie Alexander graduated in the class of 1884, writing a thesis on "The Vascular Mechanism" She earned a middle rank of "Meritorious" (between "Satisfactory" and "Distinguished") in her class.
While attending medical school in Philadelphia, many of the female medical students, including Annie, often experienced verbal abused from their male counterparts attending nearby Jefferson Medical College. She recalled one incident that occurred shortly before her graduation. Three male medical students stood near the entrance of the Women’s Medical College. When she walked up and began to enter the building, the men crossed the street in a dramatic fashion and the last man turned and spat in her direction.