He is a professor of molecular neurobiology and biophysics at Rockefeller University who won the Nobel Prize in Chemistry together with Peter Agre in 2003 for his work on the structure and operation of ion channels.

MacKinnon then transferred to Brandeis University after one year, and there he received a bachelor's degree in biochemistry in 1978, studying calcium transport through the cell membrane for his honors thesis in Christopher Miller's laboratory.

[5] In 1989 he was appointed assistant professor at Harvard University[6][7] where he studied the interaction of the potassium channel with a specific toxin derived from scorpion venom, acquainting himself with methods of protein purification and X-ray crystallography.

In 1996 he moved to Rockefeller University as a professor and head of the Laboratory of Molecular Neurobiology and Biophysics where he started to work on the structure of the potassium channel.

[12] MacKinnon is co-inventor with his friend and scientific collaborator, neurobiologist Bruce Bean of Harvard Medical School, of a dietary supplement for treating and preventing muscle cramps; they tested it in clinical trials and are co-founders a company to commercialize their invention, Flex Pharma.