This study advances understanding of gender pay gaps by examining organizational variation. The gender pay gap literature supplies mechanisms but does not attend to organizational variation; the gender and science literature provides insights on the role of masculinist culture in disciplines but misses pay gap mechanisms. A data set of federal workers allows comparison of men and women in the same jobs and workplaces. Agencies associated with traditionally masculine (engineering, physical sciences) and gender-neutral (biological, interdisciplinary sciences) fields differ. Pay-gap mechanisms vary: human capital differences explain a larger share in gender-neutral agencies, while at male-typed agencies men are frequently paid more than women within the same job. Although beyond the federal workers’ standardized pay scale, some interdisciplinary agencies more often pay men off grade, leading to higher earnings for men. Our theory of organizational variation helps explain local agency variation and how pay practices matter in specific organizational contexts.