Though a plethora of functional magnetic resonance imaging (fMRI) studies explored the neurobiological underpinnings of borderline personality disorder (BPD), findings across different tasks were divergent. We conducted a systematic review and activation likelihood estimation (ALE) meta-analysis on the fMRI studies conducted in BPD patients compared to healthy controls (HC). We systematically searched PubMed and PsychINFO from inception until July 9th 2020 using combinations of database-specific terms like 'fMRI', 'Neuroimaging', 'borderline'. Eligible studies employed task-based fMRI of the brain in participants of any age diagnosed with BPD compared to HC, during any behavioral task and providing a direct contrast between the groups. From 762 entries, we inspected 92 reports full-texts and included 52 studies (describing 54 experiments). Across all experiments, the HC > BPD and BPD > HC meta-analyses did not yield any cluster of significant convergence of differences. Analyses restricted to studies of emotion processing revealed two significant clusters of activation in the bilateral hippocampal/amygdala complex and anterior cingulate for the BPD > HC meta-analysis. Fail-safe N and single study sensitivity analysis suggested significant findings were not robust. For the subgroup of emotional processing experiments, on a restricted number of experiments providing results for each group separately, another meta-analysis method (difference of convergence) showed a significant cluster in the insula/inferior frontal gyrus for the HC > BPD contrast. No consistent pattern of alteration in brain activity for BPD was evidenced suggesting substantial heterogeneity of processes and populations studied. A pattern of amygdala dysfunction emerged across emotion processing tasks, indicating a potential pathophysiological mechanism that could be transdiagnostic.