Attending to the affect of minoritized students now appears crucial to promoting just and dignity‐affirming science education. Yet, elevating affect as an objective of science learning has a history that predates equity reforms. This study explores the politics of scientific uptakes of affect that have long served to mark hierarchical differences between students. As part of the special issue Centering Affect and Emotion Toward Justice and Dignity in Science Education, this paper investigates how U.S. science classrooms became sites of affective intervention, especially aimed at Black, Mexican American, Puerto Rican, and Indigenous students. As a history of the present, the study examines research journals and curricular reform materials between the 1954 Brown desegregation ruling and a 1989 equity report. The analysis suggests that shifts in post‐Brown U.S. science education made it possible to order students along affective hierarchies that: (1) established differential emotional regimes for those classified as ‘culturally deprived’ versus ‘gifted’; (2) equated human dignity with developing a depoliticized scientific self; and (3) evaded questions of racism and cultural imposition, while enforcing onto‐epistemic hierarchies. The study explores implications for current science education scholarship by considering how three extant concerns—deficit discourses, the dichotomization of science from political activism, and assimilationist models of scientist‐like affect—stem in part from the field's own responses to racial desegregation and civil rights demands. The purpose of historicizing affect in science education is to unsettle the racializing premises, normalizing constructs, and depoliticizing effects of social science techniques inherited from our not‐so‐distant past.