Accumulating evidence suggests that the menstrual cycle and its endogenous ovarian hormones, including progesterone (PROG) and estradiol (E2), affect cognitive performance in women, particularly by modulating the prefrontal regions. In this study, we investigated whether differences in PROG and E2 levels modulate attentional control by affecting the prefrontal cognitive control areas. An fMRI scan was conducted on 53 naturally cycling healthy women in their late follicular phase (FP, n = 28) or mid-luteal phase (LP, n = 25) to examine the resting and task states during the completion of a face‒gender Stroop task. PROG was found to be positively correlated with the nodal efficiency of the inferior frontal gyrus (IFG) in the resting-state executive control network. At the behavioral level, while accuracy in categorizing male faces remained similar, participants in the mid-LP were significantly more accurate in categorizing female faces than those in the late FP. At the neural level, both the univariate and multivariate results indicated that higher levels of PROG enhance the detection and resolution of female incongruent faces through the activation of the bilateral IFG. These findings expand evidence of the effects of ovarian hormones on prefrontal-based attentional control in the social context.