Maclean's Magazine has ranked St. Francis Xavier as the top "Primarily Undergraduate" university in Canada for five consecutive years (2002, 2003, 2004, 2005, 2006). The university has also ranked first in alumni support for the period 2001–06. In 2007, Maclean's changed the criteria of the "Primarily Undergraduate", resulting in St. Francis Xavier placing third in the category. In early 2009, Maclean's reported that St. Francis Xavier students ranked first in choosing to return to their current institution among other categories.
Between the years 2000 and 2004, more St Francis Xavier students, on a per capita basis, have received Natural Sciences and Engineering Research Council (NSERC) awards for post-secondary study than any other university in Canada.
St Francis Xavier University is organized into the Faculty of Arts, Faculty of Science, the Gerald Schwartz School of Business, Faculty of Education, and Coady International Institute. Each faculty has subordinate departments under its administration appropriate to each discipline, for example the Department of Philosophy is part of the Faculty of Arts. Faculties are headed by a dean elected from among the constituent professors.
The Faculty of Arts encompasses the following departments and programs: Anthropology, Aquatic Resources, Fine Arts, Canadian Studies, Catholic Studies, Celtic Studies, Classical Studies, Development Studies, Economics, English, History, Humanities Colloquium, Modern Languages, Philosophy, Political Science, Psychology, Religious Studies, Social Justice Colloquium, Sociology, Women's and Gender Studies, Music and Jazz Studies (The first bachelor's degree in Jazz Studies in all of Canada).
The Faculty of Science offers the following departments and programs: Aquatic Resources, Biology, Chemistry, Computer Science, Earth Sciences, Engineering, Environmental Sciences, Human Kinetics, Human Nutrition, Mathematics and Statistics, Nursing and Physics.
The Gerald Schwartz School of Business offers degrees in Business Administration, with majors in Accounting, Enterprise Development, Finance, Information Systems, Leadership in Management, and Marketing.
The Faculty of Education offers degrees in Adult Education and Education.
The Music Department hosts one of North America's leading undergraduate jazz studies program.
The current Dean of Arts is Dr. Richard Nemesvari, the Dean of Science is Dr. Petra Hauf, the Dean of Business is Dr. Tim Hynes, and the Dean of Education is Dr. Jeff Orr.
The university offers also graduate programs leading to Master of Science (M.Sc.) and Master of Education (M.Ed.) degrees.