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Evidence indicates meditation facilitates affective regulation and reduces negative affect. It also influences resting-state functional connectivity between affective networks and the posterior cingulate (PCC)/precuneus, regions critically implicated in self-referential processing. However, no longitudinal study employing active control group has examined the effect of meditation training on affective processing, PCC/precuneus connectivity, and their association. Here, we report that eight-week meditation, but not relaxation, training ‘neutralized’ affective processing of positive and negative stimuli in healthy elderly participants. Additionally, meditation versus relaxation training increased the positive connectivity between the PCC/precuneus and the pons, the direction of which was largely directed from the pons to the PCC/precuneus, as revealed by dynamic causal modeling. Further, changes in connectivity between the PCC/precuneus and pons predicted changes in affective processing after meditation training. These findings indicate meditation promotes self-referential affective regulation based on increased regulatory influence of the pons on PCC/precuneus, which new affective-processing strategy is employed across both resting state and when evaluating affective stimuli. Such insights have clinical implications on interventions on elderly individuals with affective disorders., Highlights • Meditation training in the elderly “neutralized” affective processing • Meditation training in the elderly increased pons-to-PCC resting-state connectivity • Meditation promotes affective regulation via increased influence of pons on PCC. As an increasingly popular practice, meditation is considered to facilitate affective regulation and positive mind state. Here we report meditation training versus active control ‘neutralized’ elderly participants' positive and negative affective processing, and led to more positive resting-state connectivity from the pontine nuclei, which regulates affective processing, to the posterior cingulate/precuneus which engages in self-referential processing. Further, the change in pons-to-posterior cingulate connectivity predicted change in affective processing in the meditation, but not active control, group. These findings indicate that meditation enhances affective regulatory capacities, with a neural basis of increased influence of the pontine nuclei on the posterior cingulate/precuneus.