District of Columbia Budget Autonomy Act of 2003 - Amends the District of Columbia Home Rule Act to provide that the District of Columbia budget passed by the Council of the District of Columbia shall be enacted without referral to the President or approval by the Congress, unless it is the budget for a fiscal year which is a control year. Prohibits the Mayor of the District during a control year from transmitting the budget, or amendments or supplements thereto, to the President until the completion of the budget procedures contained in this Act and the District of Columbia Financial Responsibility and Management Assistance Act of 1995.
Prohibits obligations or expenditures by District government officers and employees without the Council's approval and in the case of a control year, congressional approval.
Allows the Council to reenact provisions of any line-item veto by the Mayor in a budget Act without submitting such veto to the President, unless such item or provision is contained in a budget act for a control year.
Permits hiring of full or part-time District government employees and their transfer among programs only if such position is authorized by an Act of the Council or, in the case of a control year, an Act of Congress.