Isaiah Bowman, at the meeting of the Advisory Board of the School of Engineering on April 12, 1946, raised the question of establishing a department of Aeronautical Engineering in the School of Engineering. The committee appointed to study the prospects of organizing such a department recommended the establishment of a "Department of Aeronautics" geared toward graduate study and research. President Bowman invited Francis H. Clauser to chair the new department. No classes were offered in 1946-1947 as Professor Clauser organized the department, including the addition of two other faculty members, Guy L. Bryan and Stanley Corrsin. The department from its inception worked closely with research institutions and government laboratories such as the Applied Physics Laboratory, the Aberdeen Proving Ground, and the Naval Ordnance Laboratory. Personnel from these laboratories gave specialized courses to students at Hopkins. The link between the government and the department remained strong, and government contracts were an important source of research funding for the department. For example, the Navy funded a supersonic wind tunnel, which the department considered necessary to conduct its aerodynamic research. Built between 1948 and 1951, the wind tunnel was housed in the Aeronautics Building, now known as Merryman Hall.

In 1950 Leslie G. Kovasznay was appointed to the faculty, and Mark Morkovin and Robert Betchov were appointed as research scientists in 1951 and 1956 respectively. Faculty, staff and graduate students carried on a great deal of research in laboratories under the auspices of the department; this continued advanced work remained of primary importance to the department and helped to bring the Hopkins faculty and department to national prominence in the field of aeronautics. Upper-level undergraduate courses were eventually offered by the department, but were limited to students who were advanced in the engineering curriculum; a bachelors degree in Aeronautics was never offered.

Professor Clauser and the department participated in a number of episodes of the "Hopkins Science Review," including, "Flight at Supersonic Speeds," aired on February 2, 1949, and a series of three programs, "Man Will Conquer Space," aired in October 1952. The last of these three shows featured Wernher von Braun as the guest. The department's role included helping the producer and host prepare for the technical aspects of the program, obtaining models, diagrams and such for the show, and securing guests.

In order to advance Hopkins's program in Mechanics, the Chairmen of the Departments of Aeronautics, Civil Engineering and Mechanical Engineering jointly proposed at the Advisory Board Meeting on May 3, 1960, that the three departments merge to form a Department of Experimental and Theoretical Mechanics. The Advisory Board unanimously passed the motion, adopting the name Department of Mechanics.