Ferguson was a lecturer in anatomy at Queen's University Belfast from 1979 to 1984. In 1984 he was appointed professor of basic dental sciences in the School of Biological Sciences at the University of Manchester, at the age of thirty he was the University's youngest professor. He was director of the Dental Research Laboratories and in 1985 was awarded the Conway Medal of the Royal Academy of Medicine in Ireland. In 1986 he was appointed head of the Department of Cell and Structural Biology at the University of Manchester and from 1994 to 1996 was the dean of the School of Biological Sciences. In 1999, Ferguson was awarded a CBE for services to the Health and Life Sciences Foresight Panel.