Race disparities in behavior may emerge in several ways, some of which may be independent of implicit bias. To mitigate the pernicious effects of different race disparities for racial minorities, we must understand whether they are rooted in perceptual, affective, or cognitive processing with regard to race perception. We used fMRI to disentangle dynamic neural mechanisms predictive of two separable race disparities that can be obtained from a trustworthiness ratings task. Increased coupling between regions involved in perceptual and affective processing when viewing Black versus White faces predicted less later racial trust disparity, which was related to implicit bias. In contrast, increased functional coupling between regions involved in controlled processing predicted less later disparity in the differentiation of Black versus White faces with regard to perceived trust, which was unrelated to bias. These findings reveal that distinct neural signatures underlie separable race disparities in social cognition that may or may not be related to implicit bias.