In the summer of 1889 she read a newspaper account of the opening of the new Johns Hopkins Hospital Training School for Nurses in Baltimore, Maryland. She entered the school in October of that same year, one of seventeen in its first class. After graduation she stayed on as head nurse, then became assistant superintendent of nurses, and eventually superintendent of nurses and principal of the training school.

In 1896, she presented her first study to the American Society of Superitendents of Training Schools for nurses, in which she showed that nurse training schools were being used for little more than a means of providing hospitals with an economical workforce. Thus began her lifelong crusade to bring the education of nurses within universities.  In 1901, she was the first to develop a sound, carefully planned six-month preliminary program for nursing students. Her own scholarly approach to problems also gave her a special interest in creating a library, including material on the history of nursing. From this interest, grew the four-volume set History of Nursing (1907-1912) co-authored by Nutting and Lavinia L. Dock. Also, to meet basic professional needs, she helped establish the American Journal of Nursing (1900). 

In Maryland, she organized and was the first president of the State Association of Graduate Nurses (1903) and helped draft the state's first nurse-practice law (1904). In 1907, Nutting left Johns Hopkins to accept a full-time professorship in institutional management at Teachers College, the first nurse to be appointed to a university chair. During World War I, she was chairperson of the Committee on Nursing of the General Medical Board of the Council of National Defense, responsible for coordinating and increasing nursing resources. In addition, her own monograph, Educational Status of Nursing (1912), prepared for the Federal Bureau of Education, has been called one of the "seven historic publications by which the nursing profession now measures its progress." Moreover, as chairperson of the Education Committee of the National League of Nursing Education, Nutting led a project that resulted in publication of the Standard Curriculum for Schools of Nursing (1917).

Nutting's honors included the Liberty Service medal (World War I) of the National Institute of Social Sciences, an Honorary M. A. from Yale University in 1922, the honorary presidency of the Florence Nightingale International Foundation (1934), and the Mary Adelaide Nutting Medal (established in her honor in 1944) of the National League of Nursing Education. 

Through her work at Johns Hopkins Hospital and at Teachers College, Nutting exerted perhaps a greater influence on the development of nursing education than any other individual of her time.