Science and politics often interact successfully in administrative law. Potential problems arise, however, when agencies make “counter-scientific” policy decisions — decisions that overlook otherwise uncontroverted scientific evidence in favor of political rationales. This short essay draws new attention to these counter-scientific policy determinations by asking if and under what circumstances they may be considered illegitimate in a constitutional democracy. More specifically, it asks how counter-scientific decisions impact three of the animating principles of administrative legitimacy — agency expertise, accountability and transparency, and efficiency — and identifies some additional variables that are useful to that analysis. Part II offers recent examples of three different forms of counter-scientific policy decisions. Part III outlines the three principles of legitimacy to be applied to those decisions. Part IV then evaluates counter-scientific policy decisions in light of each of those three principles, arguing that variables such as the scope of a particular agency’s expertise, the nature of that agency and its role in government, and the agency’s own claims as to how it is exercising its policymaking authority are critical to understanding the democratic viability of counter-scientific policy decisions. This insight is not only valuable in its own right, but also as a useful starting point in a more rigorous evaluation of counter-scientific agency decisions that could have powerful implications for policymaking as well as for administrative legitimacy in general.