Dr. MacDonald was born in Toronto, Canada, educated at Upper Canada College, studied medicine at Toronto University, and received a medical degree from New York University. He later studied law at NYU, received a L.L.B. degree in 1881, and later chaired the Department of Jurisprudence.
In 1871, Dr. MacDonald was appointed Chief of Staff at the Blackwell’s Island Hospital for Epileptics and Paralytics and, four years later, became Medical Superintendent of the New York City asylums on Blackwell’s, Ward's, and Hart’s Islands. He helped establish a farm colony at Central Islip, which opened for patients in 1889.
In 1896, the city asylums were transferred to the state care system, and Dr. MacDonald was made General Superintendent for the above-named branches. He successfully advocated and fought for the poor and friendless who were committed to his care. He represented this country at several international medical congresses.
Dr. MacDonald was President of the American Medico-Psychological Association (1903–04).