The United States Department of Defense (DoD) has a complex organizational structure. It includes the Army, Navy, the Marine Corps, Air Force, Space Force, the Unified combatant commands, U.S. elements of multinational commands (such as NATO and NORAD), as well as non-combat agencies such as the Defense Intelligence Agency and the National Security Agency. The DoD's annual budget was roughly US$496.1 billion in 2015. This figure is the base amount and does not include the $64.3 billion spent on "War/Non-War Supplementals". Including those items brings the total to $560.6 billion for 2015.

Civilian control over matters other than operations is exercised through the three service departments, the Department of the Army, the Department of the Navy (which includes the Marine Corps), and the Department of the Air Force (which includes the Space Force). Each is led by a military secretary, who is below Cabinet rank.

During peacetime the Department of Homeland Security has operational and administrative control over the Coast Guard. During a national emergency the President may give operational control to the Department of Defense and administrative control to the Department of the Navy, this can also be done when Congress declares war. Prior to the creation of DHS, the Coast Guard was under the control of the Department of Transportation, and earlier under the Department of the Treasury. According to the U.S. Code, the Coast Guard is at all times considered one of the six armed services of the United States. During times of declared war (or by Congressional direction), the Coast Guard operates as a part of the Navy; this has not happened since World War II, but members have served in undeclared wars and conflicts since then while the service remained in its peacetime department.

The Pentagon Reservation in Arlington County, Virginia, across the Potomac River from Washington, D.C., is the Department's headquarters. The Department is protected by the Pentagon Force Protection Agency, which ensures law enforcement and security for the Pentagon and various other jurisdictions throughout the National Capital Region (NCR).

Chain of Command

The President of the United States is, according to the Constitution, the "Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States," now understood to also include the Air Force and other components of the DOD;Article 2 of the United States Constitution, Clause II, Section I. and Chief Executive of the Federal Government. The Secretary of Defense is the "Principal Assistant to the President in all matters relating to the Department of Defense", and is vested with statutory authority () to lead the Department and all of its component agencies, including military command authority second only to the President.

The President and the Secretary of Defense exercise authority and control of the Armed Forces in two ways: operational, and administrative. Operational command () runs from the President, through the Secretary of Defense, to the Unified Combatant Commanders for missions and forces assigned to their commands. Administratively, authority runs from the President through the Secretary of Defense to the Secretaries of the Military Departments, i.e., the Secretary of the Army (), the Secretary of the Navy (), and the Secretary of the Air Force (). The Military Departments, organized separately within the Department, operate under the authority, direction, and control of the Secretary of that Military Department. The Secretaries of the Military Departments exercise authority through their respective Service Chiefs (i.e., Chief of Staff of the Army, Commandant of the Marine Corps, Chief of Naval Operations, Chief of Staff of the Air Force, and Chief of Space Operations) over forces not assigned to a Unified Combatant Command. Except as otherwise prescribed by law, the Service Chiefs perform their duties under the authority, direction, and control of the Secretaries of their respective Military Departments, to whom they are directly responsible.

In the Goldwater-Nichols Department of Defense Reorganization Act of 1986, Congress clarified the command line to the Unified Combatant Commanders and preserved civilian control of the military. The Act states that the operational chain of command runs from the President to the Secretary of Defense to the Unified Combatant Commanders. The Act permits the President to direct that communications pass through the Chairman of the Joint Chiefs of Staff from the Secretary of Defense and the Unified Combatant Commanders. This authority places the Chairman in the communications chain. Further, the Act gives the Secretary of Defense wide latitude to assign the Chairman oversight responsibilities for the Unified Combatant Commanders' activities.

Civilian control Article II Section 2 of the Constitution designates the President as "Commander in Chief" of the Army, Navy and state militias. The President exercises this supreme command authority through the civilian Secretary of Defense, who by federal law is the head of the department, has authority direction, and control over the Department of Defense, and is the principal assistant to the President in all matters relating to the Department of Defense.10 U.S.C. 113 The Secretary's principal deputy is the equally civilian Deputy Secretary of Defense who is delegated full powers to act for the Secretary of Defense. The Office of the Secretary of Defense (OSD) is the Secretary and Deputy Secretary's civilian staff, which includes several Under Secretaries and Assistant Secretaries of Defense with functional oversight responsibilities. The Secretaries of the Military Departments (i.e. Secretary of the Army, Secretary of the Navy, and Secretary of the Air Force) are subordinate to the Secretary of Defense. They have the authority under Title 10 of the United States Code to conduct all the affairs of their respective departments (Department of the Army, Department of the Navy, and Department of the Air Force) within which the military services are organized.10 U.S.C. §§ 3013, 5013 & 8013 Although subordinate to the Secretary of Defense, they are appointed by, and serve at the pleasure of, the President of the United States. As such, they cannot be removed from office by the Secretary of Defense, but can only be removed unilaterally by the President, or through impeachment by the Congress.

Historically, there have been challenges to civilian control. Most notably, during the Korean War, General Douglas MacArthur ignored civilian instructions regarding advancing troops toward the Yalu River, which triggered an introduction of massive forces from China. Also, on April 5, 1950, Representative Joseph William Martin Jr., the Minority Leader of the United States House of Representatives, released copies of a letter from MacArthur critical of President Harry S. Truman's limited-war strategy to the press and read it aloud on the floor of the house. President Truman relieved MacArthur of command, and MacArthur then explored political options against Truman. The Revolt of the Admirals is another example in the same era of a challenge to civilian control.

DoD policies and directives protect the policy of civilian control by establishing strict limitations on military members' political activities. For example, DoD Directive 1344.10 prohibits active-duty members of the military from running for office or making political appearances in uniform. However, enforcing this strict separation between the military and politics has been problematic. For example, over the years, many elected officials, including members of Congress, continued serving in the reserves while holding elected office. As another example, at a September 14, 2007, rally for Republican Presidential candidate John McCain in New Hampshire, seven on-duty uniformed Army personnel addressed the gathering. As another example, although DOD Directive 1344.10 prohibits political appearances by active-duty military members in uniform, Virginia Governor Bob McDonnell invited a uniformed Army Staff Sergeant to stand behind him during his televised Republican response to the 2010 State of the Union Address.

Components of the Department of Defense

Program Secretary of Defense Deputy Secretary of Defense Defense Innovation UnitAssistant to the Secretary of Defense for Public Affairs*Defense Media ActivityDirector of Administration and Management*Pentagon Force Protection Agency*Washington Headquarters ServicesAssistant Secretary of Defense for Legislative AffairsDirector of Cost Assessment and Program EvaluationOffice of Net AssessmentGeneral Counsel of Defense*Defense Legal Services AgencyChief Digital and Artificial Intelligence OfficeChief Information Officer *Defense Information Systems AgencyOperational Test and Evaluation DirectorateUnited States Department of the ArmyUnited States Department of the NavyUnited States Department of the Air ForceJoint Chiefs of Staff Acquisition and SustainmentUnder Secretary of Defense for Acquisition and SustainmentDeputy Under Secretary of Defense for Acquisition and Sustainment Assistant Secretary of Defense (Acquisition)*Defense Contract Management Agency*Defense Acquisition University *Joint Rapid Acquisition Cell Assistant Secretary of Defense (Sustainment)*Director of the Office of Economic Adjustment*Director of the Defense Logistics AgencyAssistant Secretary of Defense for Energy, Installations, and Environment/Chief Sustainability Officer*Office of Local Defense Community Cooperation (OLDCC) Assistant Secretary of Defense (Nuclear Deterrence, Chemical, and Biological Defense Policy and Programs)*Defense Threat Reduction Agency Assistant Secretary of Defense for Industrial Policy*Office of Small Business Programs Joint Production Accelerator Cell Director of Special ProgramsResearch and EngineeringUnder Secretary of Defense for Research and Engineering Deputy Under Secretary of Defense for Research and EngineeringAssistant Secretary of Defense for Science and TechnologyAssistant Secretary of Defense for Critical TechnologiesAssistant Secretary of Defense for Mission CapabilitiesMissile Defense AgencyDARPA PolicyUnder Secretary of Defense for Policy Deputy Under Secretary of Defense for Policy Assistant Secretary of Defense (Strategy, Plans, and Capabilities) Assistant Secretary of Defense (International Security Affairs)*Secretary of Defense Representative in the United States Mission to NATO*Secretary of Defense Representative to the Organization for Security and Co-operation in Europe Assistant Secretary of Defense (Homeland Defense) and Global Strategic Affairs Assistant Secretary of Defense (Special Operations and Low-Intensity Conflict) Assistant Secretary of Defense (Indo-Pacific Security Affairs) Defense POW/MIA Accounting Agency Defense Security Cooperation Agency Defense Policy Board Advisory Committee Defense Technology Security Administration ComptrollerUnder Secretary of Defense (Comptroller)/CFO Deputy Under Secretary of Defense (Comptroller) Deputy Comptroller (Program/Budget) Deputy Comptroller (Budget and Appropriation Affairs)Deputy Comptroller (Enterprise Financial Transformation)Deputy Chief Financial OfficerDirector, Human Capital and Resource ManagementDefense Contract Audit AgencyDefense Finance and Accounting Service Personnel and ReadinessUnder Secretary of Defense for Personnel and Readiness