Qualifying Therapeutic Discovery Project Tax Credit Extension Act of 2013 - Amends the Internal Revenue Code to make permanent the authority to invest in and allocate credit amounts for a qualifying therapeutic discovery project (a project that is designed to: (1) treat or prevent diseases by conducting pre-clinical activities, clinical trials, and clinical studies or by carrying out research projects to approve new drugs or other biologic products; (2) diagnose diseases or conditions to determine molecular factors related to diseases or conditions; or (3) develop a product, process, or technology to further the delivery or administration of therapeutics). Extends the $1 billion allocation for such credit for each 2-year period beginning after 2013 and provides for a biennial inflation adjustment to such allocation amount after 2015.