•The neurobiological mechanisms of prefrontal tDCS remain elusive.•Meta-analyses are conducted to probe whether prefrontal tDCS modulates functional connectivity, neural oscillation and synaptic plasticity.•Anodal tDCS over the lateral prefrontal cortex significantly enhances brain activity in the frontal midline ventral attention network (VAN).•Brain activity increment positively correlates with current density at the stimulating electrode and current strength in the median cingulate.•Anodal tDCS over hippocampus/prefrontal cortex enhances LTP formation and brain BDNF expression over the stimulated brain region in rodents. The neurobiological mechanisms underlying prefrontal transcranial direct current stimulation (tDCS) remain elusive. Randomized, sham-controlled trials in humans and rodents applying in vivo prefrontal tDCS were included to explore whether prefrontal tDCS modulates resting-state and event-related functional connectivity, neural oscillation and synaptic plasticity. Fifty studies were included in the systematic review and 32 in the meta-analyses. Neuroimaging meta-analysis indicated anodal prefrontal tDCS significantly enhanced bilateral median cingulate activity familywise error (FWE)-corrected p < .005; meta-regression revealed a positive relationship between changes in median cingulate activity after tDCS and current density (FWE-corrected p < .005) as well as electric current strength (FWE-corrected p < .05). Meta-analyses of electroencephalography and magnetoencephalography data revealed nonsignificant changes (ps > .1) in both resting-state and event-related oscillatory power across all frequency bands. Applying anodal tDCS over the rodent hippocampus/prefrontal cortex enhanced long-term potentiation and brain-derived neurotrophic factor expression in the stimulated brain regions (ps <.005). Evidence supporting prefrontal tDCS administration is preliminary; more methodologically consistent studies evaluating its effects on cognitive function that include brain activity measurements are needed.