Preclinical studies demonstrate that chronic stress modulates the effects of oestradiol (E2) on behaviour through the modification of the amygdala and the medial prefrontal cortex (mPFC) neuronal structure. Clinical studies suggest that alterations in amygdala functional connectivity (FC) with the mPFC may be associated with stress‐related phenotypes, including mood and anxiety disorders. Thus, identifying the effects of stress and E2 on amygdala‐mPFC circuits is critical for understanding the neurobiology underpinning the vulnerability to stress‐related disorders in women. In the present study, we used a well‐validated rhesus monkey model of chronic psychosocial stress (subordinate social rank) to examine effects of E2 on subordinate (SUB) (i.e. high stress) and dominant (DOM) (i.e. low stress) female resting‐state amygdala FC with the mPFC and with the whole‐brain. In the non‐E2 treatment control condition, SUB was associated with stronger left amygdala FC to subgenual cingulate (Brodmann area [BA] 25: BA25), a region implicated in several psychopathologies in people. In SUB females, E2 treatment strengthened right amygdala‐BA25 FC, induced a net positive amygdala‐visual cortex FC that was positively associated with frequency of submissive behaviours, and weakened positive amygdala‐para/hippocampus FC. Our findings show that subordinate social rank alters amygdala FC and the impact of E2 on amygdala FC with BA25 and with regions involved in visual processing and memory encoding.