Unintentional weight loss is a major frailty component; thus, assessing energy imbalance is essential for institutionalized elderly residents. This study examined prediction errors of the observed energy intake (OEI) against the actual energy intake obtained from the doubly labeled water (DLW) method and clarified the relationship between the energy gap obtained by subtracting total energy expenditure (TEE) from OEI and subsequent weight changes in elderly residents in long-term care facilities. Overall, 46 participants were recruited in Japan. TEE was measured using the DLW method, and OEI was calculated from recipes and plate waste simultaneously over a 14–15-day period at baseline. The total energy intake (TEIDLW) was determined on the basis of DLW and weight changes during the DLW period. The weight was longitudinally tracked monthly for 12 months in the 28 residents who still lived at the facilities. OEI was higher than TEIDLW by a mean of 232 kcal/day (15.3%) among 46 residents at baseline. The longitudinal data of 28 residents showed that the energy gap tended to be correlated with the slope of weight change (ρ = 0.337, p = 0.080) and the median value was significantly lower in the weight loss group (152 kcal/day) than in the weight gain group (350 kcal/day) (p < 0.05). In conclusion, weight loss could occur at Japanese long-term care facilities even if the difference obtained by subtracting TEE from OEI was positive because OEI was overestimated by more than 200 kcal/day.