Discussions about congressional earmarking often focus on their direct costs in the federal government’s appropriations bills. This article shows that this conventional view neglects the administrative costs of earmarking by examining the extensive transaction and opportunity costs that come with the political, budgetary, and programmatic management of these earmarked projects in Congress and in the Office of Naval Research. One policy conclusion from this study is that the executive branch should make these costs transparent, as they remain largely hidden from public discussion and the consideration of the federal budget.