The Rector's Division is responsible for the realization of the goals and objectives of the Colegio in the light of its Philosophy, Vision and Mission. It therefore, sets strategies for Letran's continuous search for excellence.

The Rector's office being at the helm of the institution provides leadership to other sectors of the community. The Rector, as the chief executive officer of the Colegio, acts and decides for and on behalf of the board of trustees on important and urgent matters that concerns the Colegio. He sees to it that Guiding principles are integrated with institutions programs and activities. The Rector also chairs the Economic, Religious and the Academic Councils. Together with the other offices under the Rector's Division, the Rector carefully plans to have an effective, functional and operational organizational structure of the whole community.

Being a Catholic educational institution, the Colegio puts premium on the spiritual development of its students and employees. The Religious Affairs Division is tasked to provide plans and programs in order for its students and employees to live in the values and ideals the Colegio wishes them to acquire.

The Religious Affairs Division is headed by the Vice Rector for Religious Affairs. Each Academic department has their respective Chaplain who determines course of action to meet their student's needs in spiritual formation

The Academic Affairs Division is the division tasked to oversee the academic operations of the Colegio. It provides strategic directions to the academic development programs set by the school. Being the heart and soul of the academic, it never ceases to improve the School's academic standard.

The Academic Affairs Division is headed by the Vice-Rector for Academic Affairs. He is being assisted by the Principal of the Elementary and High School departments, and by the dean of the College of Business Administration and Accountancy, College of Liberal Arts, Sciences and Education, the Graduate School of Business Administration. Each academic head develops plans, programs, policies, systems and methods necessary for the attainment of the objectives of their respective department.

The Financial Affairs Division sets strategic direction of the financial operations of the Colegio. It provides plans and programs for the effective and useful operations of the Colegio's resources. Every now and then, this division assesses the financial status of the Colegio and always considers the budgetary system as an indispensable tool for the formulation of plans and realization of the Colegio's mission and objectives. 

The Vice-Rector for Financial Affairs is the head of the Financial Affairs Division with the Assistant Treasurer at his side.

The Support Services Division primarily provides support and assistance to the students in their academic and various needs. It continuously seeks improvement in giving high-quality and up-to-date facilities and resources materials that will best facilitate learning. The support services identified their goals in promoting commitment to the delivery of quality service to the students and community as well.

The Vice-Rector for support services as the head of Support Services Division oversees the long-range and short-range plans of the offices under the division.