Office of the Secretary – Proper. Advise the President on matters related to education; Establish the policies and standards for the operation of the Department pursuant to the approved programs of the government; Promulgate rules and regulations necessary to carry out the objectives, policies, functions, plans, programs and projects of the Department; Promulgate issuances necessary for the efficient administration of the offices under him and proper implementations of laws relative to education; Exercise disciplinary powers over officials and employees in accordance with existing laws; Formulate and enforces a management control system to measure and evaluate performance of the Department and submits periodic reports to the President; Prepare and submits to the President through the Department of Budget and Management the budget of the Department; and, appoint all officers and employees of the Department except those whose appointment is vested in the President.

Office of the Undersecretaries. Advise and assist the Secretary in the formulation and implementation of Department policies, plans and programs; Oversee all the operational activities of the Department policies, plans and programs; Oversee all the operational activities of the Department for which they will be assigned and held responsible by the Secretary; Coordinate the programs and projects of the Department; On the basis of an official designation, discharge temporarily the duties of the Secretary in case of latter's inability to discharge their duties or in case of vacancy of the said office.

Office of the Assistant Secretaries. Advise and assist the Secretary or Undersecretary in the formulation and implementation of Department policies, plans, and programs; Oversee all the operational activities of the Department for which they will be assigned and held responsible for by the Secretary or Undersecretary; Coordinate the programs and projects of the Department; On the basis of an official designation, discharge temporarily the duties of the Secretary or Undersecretary in case of the latter's inability to discharge their duties or in case of vacancy of the said office.

Internal Audit Service. Provides advice to the Secretary on the adequacy and effectiveness of internal controls; the 4Es (Economy, Effectiveness, Efficiency and Ethicality); degree of compliance to accountability measures, ethical standards and contractual obligations through the results of objective and systematic evaluation of operating systems/processes and programs/activities/projects (PAPs) in accordance with government internal auditing standards towards the achievement of DepEd's objectives.

Legislative Liaison Office. Recommends, coordinates, supervises and executes the legislative initiatives and priority policy reforms and development of progams of the Department of Education (DepEd) with the two Houses of Congress (House of Representatives and Senate) and other interest groups (other government and non-government agencies, education stakeholders and the PLLO) through comprehensive engagement strategies and dissemination of information of all major Executive-Legislative activities towards the effective and responsive implementation of the law and the corresponding IRR.

Sites Titling Office. Assures the Department of Education (DepEd) and protects its rights and interests over ownership of school sites by public and secondary schools through the titling and acquisition of properties

Literacy Coordinating Council Secretariat. Provides the LIteracy Coordinating Council and education stakeholders with technical and administrative support in policy formulation and coordination of initiatives towards universalization of literacy in the Philippines.

National Educators Academy of the Philippines. Provides for and supports the personal grwoth and professional development of teachers and school leader in the Department of Education (DepEd) through the establishment, implementation and maintenance of a Learning and Development (L&D) system that subscribes to needs and competency-based L&D paradigm to enable them to perform their roles and functions effectively and efficiently toward the attainment of quality accessible, relevant and liberating basic education for all.