When Boston College opened its doors in 1864, a year after its 1863 charter, it was a modest start with one clear purpose: to teach the humanities, social sciences and natural sciences at the heart of a Jesuit education. A "college" meant something different back then. It wasn't the sprawling university most people picture today, with its separate graduate and professional schools all under one roof. A nineteenth-century college offered a single path toward a single degree, the bachelor of arts. And it didn't necessarily serve only students fresh out of high school. Public high schools were still rare in the 1860s, so colleges commonly ran their own preparatory classes to get younger students ready for college-level work. Boston College followed that same pattern, running its own preparatory courses for nearly forty years before spinning them off in 1902 to form Boston College High School. There was, in other words, no "College of Arts and Sciences" in these early years simply because there was nothing else for it to be separate from. The College and the university were one and the same, an arrangement that held for more than half a century.

Day-to-day academic life in these early decades ran through two men rather than one: a prefect of studies and a prefect of discipline. Robert Fulton, SJ, held the first of these posts, guiding the young college's studies through its earliest years. Exactly when the College first got a dean of its own, separate from the prefects, is harder to pin down. Some accounts trace it to 1914, the year the university's presidency passed from Thomas I. Gasson, SJ, to Charles W. Lyons, SJ. Others place it closer to 1920, pointing to Patrick J. McHugh, SJ, who at his death in January 1935 was remembered as having served fifteen years as dean. Either way, McHugh stands as the College's first clearly identifiable dean, leading it through the 1920s and into the Depression years until his death in office. Graduate education would eventually become part of the College's own academic programming, but that was still decades away. For most of the twentieth century, the College and the Graduate School operated as separate schools, each with a dean of its own.

The undergraduate College saw its biggest changes at mid-century. In 1958, Latin was dropped as a degree requirement, and the College launched new Honors and Scholar of the College programs. Five years later, a sweeping self-study timed to the university's centennial reshaped the core curriculum, lightened course loads, gave faculty their first sabbaticals, and put department chairs up for election. By 1970, coeducation had reached every undergraduate program. The Music Program joined the College as a department in 1988, and in 1994, graduate programs in Nursing and Education - until then technically part of the Graduate School of Arts and Sciences - were spun off to their own professional schools.

That long-standing separation between the College and its graduate counterpart didn't last much longer. In the middle of the 2000s, Dean Joseph Quinn's departure partway through the 2006-07 academic year gave Boston College an opening to rethink the arrangement. Rather than name a new dean to a stand-alone graduate school, the university closed the Graduate School of Arts and Sciences and folded it into the College - a change that showed up within a year as a single combined unit on the university's own organizational charts. In its place came two new positions built to manage graduate education going forward: an associate dean for graduate academic affairs within the College itself, and a newly created vice provost for graduate education in the Provost's office.

David Quigley took over as dean, steering the College through the addition of new majors in Islamic Civilization and Societies and environmental studies, along with the planning of Stokes Hall. Quigley left the deanship in 2014 to become Boston College's provost, succeeding Joseph Quinn, the same dean whose departure had set the merger in motion eight years earlier. Gregory Kalscheur, SJ, who came to the role from the Law School faculty, succeeded Quigley and kept graduate education running through an associate dean rather than reviving it as a separate school.

The College took on its current name the following year. In 2015, Boston College renamed it in honor of Robert J. Morrissey, a member of the class of 1960 and a longtime university trustee, marking a philanthropic milestone for the University.