We theorized that income racial-ethnic stratification among academic scientists is perpetuated by inequality of scientific capital including institutional prestige, research funding, publishing, and tenure. We tested our model with original survey data of US biologists and physicists (n = 1,160). Findings indicated that white scientists reported higher incomes than non-white scientists despite no significant differences in productivity, funding, or institutional status. Black scientists reported earning the lowest pay, while Hispanic scientists reported incomes statistically similar to those of white scientists. We also observed racial-ethnic inequality in promotion to tenure, which indirectly contributed to racial-ethnic stratification in pay. While overrepresented in our sample relative to the US population, East Asian scientists experienced particular disadvantages in promotion. Our findings challenge the Model Minority Myth, and they have implications for our understanding of the reproduction of a racial order, even in science, a field characterized by explicit overtures of tolerance and inclusion.