DISA has a total budget of $11.9 billion and receives funding through both congressional appropriations of $3.4 billion and a Defense Working Capital Fund of $8.5 billion.

The agency is budgeted to support the IT needs and requirements of the entire Defense Department, including the offices of the secretary of defense and of the chairman and vice chairman of the Joint Chief of Staff, the Joint Staff, military services, combatant commands, and defense agencies. DISA also provides support to the White House and many federal agencies through a number of capabilities and initiatives.

DISA's Appropriated Budget

Through its appropriated budget, DISA is funded by Congress through the National Defense Authorization Act, the U.S. federal law specifying the budget and expenditures for DOD, and defense appropriations bills authorizing DOD to spend money. This budget enables the agency to implement the White House's national security strategy, the secretary's planning and programming guidance, and the initiatives of the DOD CIO.

DISA aligns its program resource structure across six mission areas, which reflect DOD's goals and allow DISA to execute its core missions and functions:

1. "Transition to the Net-Centric Environment" funds capabilities and services that transform the way that DOD shares information by making data continuously available in a trusted environment. This mission area includes enterprise services, engineering services, and technical strategies developed by DISA's chief technology officer.
2. "Eliminate Bandwidth Constraints" focuses on capabilities and services that build and sustain the Global Information Grid transport infrastructure, while eliminating bandwidth constraints and rapidly surging to meet demands. Capabilities funded in this category include the Pathways Program, DOD Teleport Program, Defense Spectrum Organization activities, and Defense Information System Network  enterprise activities, such as non-recurring costs for commercial circuits, commercial satellites, and special communications requirements.
3. "GIG Network Operations and Defense" funds the operation, protection, defense, and sustainment of the enterprise infrastructure and information-sharing services, as well as enabling command and control. This mission area includes funding for network operations ; the information assurance/public key infrastructure program; cybersecurity initiatives; and budgets for DISA's field offices, which support the combatant commands, and for the Joint Staff Support Center, which supports the chairman, vice chairman, and Joint Chiefs of Staff in the Pentagon.
4. "Exploit the GIG for Improved Decision Making" focuses on transitioning to DOD enterprise-wide capabilities for communities of interest, such as command and control and combat support, that exploit the GIG for improved decision-making. This mission area funds the Global Command and Control System – Joint program, Global Combat Support System – Joint program, and senior leader and coalition information-sharing activities.
5. "Deliver Capabilities Effectively/Efficiently" finances the means by which the agency effectively, efficiently, and economically delivers capabilities based on established requirements. This area funds the command staff and the personnel costs for DISA's shared service units.
6. "Special Mission Areas" enables the agency to execute special missions to provide the communications support required by the president as commander-in-chief, including day-to-day management, fielding, operation, and maintenance of communications and information technology. The White House Communications Agency and the Communications Management Control Activity in the Network Services Directorate are budgeted out of this mission area.

DISA's Defense Working Capital Fund

DISA also operates a DWCF budget. Unlike the appropriated budget, which is provided through direct congressional appropriations, the working capital fund relies on revenue earned from providing IT and telecommunications services and capabilities to finance specific operations. Mission partners order capabilities or services from DISA and make payment to the working capital fund when the capabilities or services are received.

A DWCF business unit is not profit-oriented and, therefore, only tries to break even, charging prices set using the full-cost-recovery principle, which accounts for all costs — both direct and indirect (or "overhead") costs. It is intended to generate adequate revenue to cover the full cost of its operations and to finance the fund's continuing operations without fiscal year limitation.

DISA operates the information services activity within the DWCF. This activity consists of two main components. The first component includes two lines of service: telecommunications services and enterprise acquisition services. The second component includes computing services.

The major element of the telecommunication services component is the Defense Information System Network, which provides interoperable telecommunications connectivity and accompanying services that allow the department to plan and operate both day-to-day business and operational missions through the dynamic routing of voice, data, text, still and full-motion imagery, and bandwidth services. Some DISN services are provided to mission partners in predefined packages and sold on a subscription basis via the DISN subscription service, while others are made available on a cost-reimbursable basis.

The line of service for enterprise acquisition services enables the department to procure best value, commercially competitive IT services and capabilities through DISA's Defense IT Contracting Organization. DITCO provides complete contracting support and services.

The computing services component of DISA's DWCF activities comprises the defense enterprise computing centers, which provide mainframe and server-processing operations, data storage, production support, technical services, and end-user assistance for command and control, combat support, and enterprise applications across DOD. These facilities and functions provide a robust enterprise computing environment to more than 4 million users through 30 mainframes, more than 7,000 servers, 8,000 terabytes of data, and approximately 450,000 square feet of raised floor.