Background Emotional eating refers to overeating triggered by emotional experiences and may cause significant psychological distress and health problems. Thus, it is important to better understand its underlying mechanisms. The study examined if the ability to ignore task-irrelevant information, namely, interference control, is modulated by mood and exposure to food stimuli among females who are high and low on emotional eating. Method The study’s sample included 80 women who were high (N = 40) or low (N = 40) on an emotional eating scale. Participants were divided to a negative or neutral mood induction group. Following the mood induction, they completed a food-flanker task that allowed assessing attentional interference caused by food and non-food stimuli separately. Results The low emotional eating group had significantly greater food compared to non-food interference, suggesting difficulty at ignoring food stimuli while attending a neutral target. In the high emotional eating group, there was no difference between food and non-food interference. However, higher levels of emotional eating predicted lower levels of food interference. Conclusion The pattern of results suggests a food-avoidance attentional tendency among those with higher levels of emotional eating. The mood manipulation did not influence food-related interference in either group. The lack of an effect of mood on food-related interference questions the impact of negative emotions on basic attentional processes among individuals with emotional eating.