In-group favoritism and prejudices relate to discriminatory behaviors but, despite decades of research, understanding of their neural correlates has been limited. A systematic coordinate-based meta-analysis of functional magnetic resonance imaging (fMRI) studies (altogether 87 original datasets, n = 2328) was conducted to investigate neural inter-group biases, i.e., responses toward in-group vs. out-group in different contexts. We found inter-group biases in some previously identified brain regions (e.g., the medial prefrontal cortex, insula) but also in many previously non-identified brain regions (e.g., the cerebellum, precentral gyrus). Sub-group analyses indicated that neural correlates of inter-group biases may be mostly context-specific. Regarding different types of group memberships, inter-group bias toward trivial groups was evident only in the cingulate cortex, while inter-group biases toward “real” groups (ethnic, national, or political groups) involved broader sets of brain regions. Additionally, there were heightened neural threat responses toward out-groups’ faces and stronger neural empathic responses toward in-groups’ suffering. We did not obtain significant publication bias. Overall, the findings provide novel implications for theory and prejudice-reduction interventions.