Short-term abstinent alcoholics have shown increased engagement of reward regions and reduced engagement of executive control regions. There is no report yet on whether these differences can predict relapse. This is the first study that investigates whether differences in resting-state networks can predict later relapse. Resting-state functional magnetic resonance imaging data were collected from 69 short-term abstinent alcoholics. Participants performed the affective go/no-go task outside of the scanner. At 6-month follow-up, participants were grouped as abstainers (N = 40; age: M = 46.70, standard deviation [SD] = 6.83) and relapsers (N = 29; age: M = 46.91, SD = 7.25). We examined baseline resting-state synchrony (RSS) using seed-based measures. Compared with abstainers, relapsers showed significantly decreased RSS within both the reward and executive control networks as well as within the visual network (P < 0.05). Lower RSS in relapsers could predict relapse (P < 0.05) and was significantly correlated with poor inhibitory control of emotional-laden stimuli (P < 0.017) and with alcohol use (P < 0.05). Results suggest that lower RSS during short-term abstinence may predict subsequent relapse. The association of lower RSS with poorer inhibitory control suggests that low RSS may constitute a faulty foundation for future responses to external cues, which can be manifested as the inability to inhibit behavior.