Foreign Aid Transparency and Accountability Act of 2013 - Directs the President to establish guidelines for the establishment of measurable goals, performance metrics, and monitoring and evaluation plans for U.S. foreign assistance.

Requires such guidelines to provide direction to federal departments and agencies that administer U.S. foreign assistance relating to: (1) resource monitoring, (2) project and program evaluation, and (3) analysis of findings and generalizations and their applicability to proposed project and program design.

Requires: (1) each appropriate federal department or agency to begin using such guidelines within one year after their establishment, and (2) the President to submit a related report to Congress within 18 months.

Directs the President to require the Secretary of State to establish and maintain an Internet website to make publicly available comprehensive and accessible information on U.S. foreign assistance programs on a country-by-country and program-by program basis. Requires the head of a federal department or agency to brief Congress if specified information requirements are not met.

Authorizes a department or agency to use up to 5% of its foreign development assistance funds for activities under this Act.