Binge Eating Disorder (BED) has been associated with deficits in cognitive control and decision-making. Yet, no study has yet investigated the characteristics of food choice and the involved choice conflict in this disorder. In the present study individuals with BED (N = 22) and without BED (N = 61), with a body mass index (BMI) between 21 and 44 completed 153 binary food decisions among foods varying in palatability and energy density. To assess conflict during choice we recorded computer mouse paths and reaction times. Subsequently, participants rated all foods on liking and energy content. Finally, participants completed a bogus taste test with the same foods to measure actual consumption. Predictors were modelled continuously using Bayesian mixed-effects modelling. Individuals with BED liked foods with higher energy content more and chose them more often in the choice task. Yet, actual consumption in the taste test did not differ between groups, neither regarding total consumption, nor of foods with higher energy. Mouse cursor-tracking revealed that control participants with higher BMIs showed more choice conflict than those with lower BMIs. This pattern was reversed in those with BED. The high-energy preference in ratings and food choice represent the first evidence in a controlled laboratory context for disorder-congruent food choice in BED. The fact that this was not reflected in actual consumption might have methodological implications for measuring laboratory eating behaviour. Mouse cursor-tracking gave further insights into choice processes and showed a less conflicted food choice in those with BED with higher BMI compared to those with lower BMI.