This meta-analysis aims to evaluate whether the extant literature justifies any definitive conclusions about whether and how SITBs may be associated with brain differences. A total of 77 papers (N = 4,903) published through January 1, 2019 that compared individuals with and without SITBs were included, resulting in 882 coordinates. A pooled meta-analysis assessing for general risk for SITBs indicated a lack of convergence on structural differences. When all types of control groups were considered, functional differences in the left posterior cingulate cortex (PCC), right amygdala, left hippocampus, and right thalamus were significant using multi-level kernel density analysis (pcorrected < 0.05) but nonsignificant using activation-likelihood estimation. These results suggest that a propensity for internally-oriented, emotional processing coupled with under-active pain processing could potentially underlie SITBs, but additional research is needed to test this possibility. Separate analyses for types of SITBs suggested that the brain differences associated with deliberate self-harm were consistent with the overall findings. Checkered moderator effects were detected. Overall, the meta-analytic evidence was not robust. More studies are needed to reach definitive conclusions about whether SITBs are associated with brain differences.