Postpartum psychosis (PP) is a severe mental disorder that affects women in the first few weeks after delivery. To date there are no biomarkers that distinguish which women at risk (AR) develop a significant psychiatric relapse postpartum. While altered brain connectivity may contribute to the risk for psychoses unrelated to the puerperium, this remains unexplored in PP. We followed up 32 AR and 27 healthy (HC) women from pregnancy to 8-week postpartum. At this point, we classified women as AR-unwell (n = 15) if they had developed a psychiatric relapse meeting DSM-IV diagnostic criteria, or impacting on daily functioning and requiring treatment, or AR-well (n = 17) if they remained asymptomatic. Women also underwent an fMRI scan at rest and during an emotional-processing task, to study within- and between-networks functional connectivity. Women AR, and specifically those in the AR-well group, showed increased resting connectivity within an executive network compared to HC. During the execution of the emotional task, women AR also showed decreased connectivity in the executive network, and altered emotional load-dependent connectivity between executive, salience, and default-mode networks. AR-unwell women particularly showed increased salience network-dependent modulation of the default-mode and executive network relative to AR-well, who showed greater executive network-dependent modulation of the salience network. Our finding that the executive network and its interplay with other brain networks implicated in goal-directed behavior are intrinsically altered suggest that they could be considered neural phenotypes for postpartum psychosis and help advance our understanding of the pathophysiology of this disorder.