The concept of a nationally supported institute for theoretical astrophysics dates back to discussions within the Canadian Astronomical Society in the early 1980s.

At the same time, Professor Richard Henriksen worked on establishing CITA, Inc. (a separate entity from CITA the institute at the University of Toronto) as an incorporated national institute and charity governed by an elected Council of Canadian astrophysics/relativity professors to promote research in theoretical astrophysics across the country.

CITA has a small number of long-term faculty members, and a larger number of short term (3- or 5-year) postdoctoral positions, as well as an active visitor program; the purpose of the relatively high influx of new researchers or visitors is to ensure that timely topics are well represented at CITA.

In 1985, Scott D. Tremaine came to CITA as its first director; Margaret Fukunaga was hired as the permanent Business Officer and Dick Bond arrived as the second faculty member.

Notable past and present faculty members of CITA also include: CITA has active research programs in cosmology (particularly in studies of the cosmic microwave background and intensity mapping), early universe studies and cosmic inflation, neutron stars (especially scintillometry and magnetars), fast radio burst, active galaxies, star formation, planet formation, gravitational waves and plasma astrophysics.