The first Dean of the College of Engineering (CEn) was Engr. Teresito Remollo who laid down the foundation for the College in its early stage of development. His achievements from the time he assumed the position in 1968 and until his retirement in 1985, gained the recognition for HAU as a foremost engineering school in the region. The work he started was continued by his predecessors. He was succeeded by Engr. Geromin T. Nepomuceno, Jr. who was Officer-in-Charge of the College from 1985 to 1987. Engr. Renato Santiago held the position of Officer-in-Charge from 1987 to 1990 and Engr. Abigail Arcilla was the Acting Dean from 1990 to 1992. Engr. Ruby P. Henson held the position of the Dean from 1992 to 1999 and then Engr. Roman A. Palo in 1999 to 2005. CEn then became CEA - College of Engineering and Architecture in 2003. Engr. Abigail P. Arcilla was the Dean in 2005 to 2010; Dr. Maria Doris C. Bacamante in 2010 to 2016.  CEA then became SEA –School of Engineering and Architecture in 2017. Dr. Ruby P. Henson was the Dean in 2016-2017; Dr. Felicito F. Caluyo in 2017-2018; and Dr. Jay Jack R. Manzano in 2018-2019.   Dr. Filipina I. De Guzman holds the deanship position from 2019 to present.

In all its years of existence, the College of Engineering has been committed to the objective of "providing well-rounded professional training to students who can make a definite contribution to the industrialization and economic progress of the Philippine through applied Science and Technology." Hence, the curricula for the different programs are so designed not only to conform to CHED, DECS-TPEAE curricular guidelines but also to ensure that Engineering graduates have the necessary academic background in terms of knowledge both in the technical and social disciplines as well as field experience for the specific area of specialization. In line with this, engineering graduates are required to undergo apprenticeship training in the industries to enhance their field of experience.

The training that engineering students obtain is further enriched by their involvement in extra-curricular activities and this is made possible through membership in student organizations. There are nine (9) student organizations based in the college most of which are accredited student chapters of national professional organizations. These are the Philippine Institute of Civil Engineers (PICE); Integrated Institute of Electrical Engineers (IIEE); Integrated Electronics and Communications Engineers of the Philippine (IECEP); Philippine Institute of Industrial Engineers (PIIE); Philippine Society of Mechanical Engineers (PSME); Institute of Computer Engineers of the Philippines (ICEPEP); United Architects of the Philippines Student Auxiliary (UAPSA); Society of Aerospace Engineers of the Philippines (SAEP) and Student Association for General Engineering (SAGE). The realization of the objectives of the college is evidenced by the growing number of engineering graduates and professionals that the institution has produced. The college also boasts of a number of engineering board topnotchers.

The College of Engineering has gone a long way since 1963. The four-storey building for the college marks the genuine commitment of HAU in strengthening engineering education. The edifice, named the Sacred Heart Building, houses lecture rooms, an audio visual room, and all the engineering laboratories as follows: Soils, Material Testing, Hydraulics, Mechatronics, Mechanical Engineering, Electrical Engineering, Electronics, Chemistry, Physics and Computer laboratories, the latter including a CADD Center, Industrial Engineering and Aeronautical Engineering. An adjacent building, called the Archbishop Pedro Santos (APS) building, houses the Drafting Rooms used by the Architecture students. Alongside the continuous upgrading of facilities, the college plans to pursue a comprehensive faculty development program in line with the objective of upgrading instruction. The college also exerts considerable effort in keeping up with the technological pace through the application of computer technology in instruction and research. Aware of the existing resources and the demand of the external environment, the activities and programs of the college are being expanded so as not to be limited to the traditional academic scope but will consider the demands of the external environment through academe-industry linkages and other forms of community involvement.

In April 1995, the programs in the College of Engineering attained FAAP second-level (II) accreditation status through PAASCU. PAASCU Re-accreditation was attained in the school year 1998-1999. The Commission on Higher Education (CHED) awarded the two programs from the College of Engineering, namely: Electrical and Industrial Engineering departments as the Centers of Development (COD) in the region. PAASCU Level III Accreditation was granted in the School Year 2004-2005 for CE, EE, IE & ME. In School Year 2009-2010, in addition to the Electrical and Industrial Engineering departments, the Civil Engineering department was also granted Center of Development (COD) by CHED.  The Computer Engineering Program was granted PAASCU Candidate Status in SY 2010-2011 which qualifies it for a formal survey visit for Level I in the following school year; and a Level II reaccredited status in February 2020. Both Architecture Program and Aeronautical Engineering Program were granted PACUCOA Level I Accreditation in 2018 and 2019, respectively.

The School of Engineering and Architecture realizes the importance of its role in present times of making engineering education relevant as it continues to support national development efforts.