Veterans Affairs Research Transparency Act of 2013 - Directs the Secretary of Veterans Affairs to make available on a publicly-available Department of Veterans Affairs (VA) website: (1) data files that contain information on VA research, (2) a data dictionary on each data file, and (3) instructions on how to obtain access to each data file for use in research.

Directs the Secretary, within 540 days after enactment of this Act, to require, as a condition on the use of any data gathered or formulated from research funded by the VA, that any final, peer-reviewed manuscript prepared for publication that uses such data be submitted to the Secretary for deposit in a digital archive (established by the Secretary under this Act). Requires such archive to be publicly available.

Requires the Department of Veterans Affairs-Department of Defense Joint Executive to submit to the Secretary and the Secretary of Defense (DOD) options and recommendations for establishing a program of long-term cooperation and data-sharing between and within the VA and DOD to facilitate research on outcomes of military service, readjustment after combat deployment, and other topics of importance to veterans, members of the Armed Forces (members), their families, and members of communities that have a significant population of veterans or members.