This study explored the effect of electroencephalographic infraslow neurofeedback (EEG ISF-NF) training on effective connectivity and tested whether such effective connectivity changes are correlated with changes in pain and disability in people with chronic low back pain. This involved secondary analysis of a pilot double-blinded randomised placebo-controlled study. Participants ( = 60) were randomised to receive ISF-NF targeting either the pregenual anterior cingulate cortex (pgACC), dorsal anterior cingulate and somatosensory cortex (dACC + S1), ratio of pgACC*2/dACC + S1, or Sham-NF. Resting-state EEG and clinical outcomes were assessed at baseline, immediately after intervention, and at one-week and one-month follow-up. Kruskal-Wallis tests demonstrated significant between-group differences in effective connectivity from pgACC to S1L at one-month follow up and marginal significant changes from S1L to pgACC at one-week and one-month follow up. Mann-Whitney U tests demonstrated significant increases in effective connectivity in the ISF-NF up-training pgACC group when compared to the Sham-NF group (pgACC to S1L at one-month ( = 0.013), and S1L to pgACC at one-week ( = 0.008) and one-month follow up ( = 0.016)). Correlational analyses demonstrated a significant negative correlation (ρ = -0.630, = 0.038) between effective connectivity changes from pgACC to S1L and changes in pain severity at one-month follow-up. The ISF-NF training pgACC can reduce pain via influencing effective connectivity between pgACC and S1L.