Data from United States Budgetary Costs and Obligations of Post-9/11 Wars through FY2020: $6.4 Trillion (2019) by Neta Crawford.
Congressional appropriations to the Pentagon from Fiscal Years 2001-2016 have totaled more than $8.5 trillion. About $6.8 trillion of this was in non-emergency, base budget appropriations, including for personnel pay and benefits, weapons procurement, and funding for military bases.
Unfortunately, because the Pentagon has not done a competent or transparent accounting for these and other appropriations, we have no reliable assurance of how, or even where, the funds were actually spent.
However, according to our estimates, the portion of the increase to Pentagon base budget from 2001-2016 that can be attributed to the War on Terror is about $733 billion.
This additional spending is most plausibly explained by the political dynamics of the post-9/11 wars that have translated into Congressional support, not just for war funding, but for the broader Department of Defense budget as well.
Pentagon accounting for the wars has been deeply inadequate, and we do not know what the DOD actually spent on the wars.
The best accounting of Pentagon appropriations is by the Congressional Research Service, showing $1.6 trillion through FY2015.
Congress should require the Department of Defense Inspector General to conduct a comprehensive audit of the actual amounts of all federal funding spent on the post-9/11 wars, and should make the report publicly available.
(Page updated as of September 2016)