The time of eating has been considered to have an important role in weight regulation. However, it is unknown if there are specific daily patterns of energy and macronutrient distribution that could be more beneficial for metabolic outcomes, especially obesity. This study aimed to assess the effect of time-of-day energy and macronutrient intake at 4 y of age on the weight status at 7 y of age. The study sample included 1961 children from the population-based birth cohort Generation XXI, with data on 3-day food diaries at 4 y and body mass index (BMI) z-scores at 7 y. Dietary patterns based on the collected data were obtained for the distribution of energy and macronutrients across eating occasions. Having a relatively higher energy intake at lunch and supper (OR = 1.19, 95% CI = 1.05 to 1.34) or at mid-afternoon (OR = 1.18, 95% CI = 1.05 to 1.34) at 4 y was associated with higher odds of becoming overweight/obese at 7 y. A relatively higher intake of fat at lunch was positively associated with later children’s odds for being overweight or obese (OR = 1.17, 95% CI = 1.03 to 1.32). These associations were independent of the effect on children’s eating behaviors related to appetite. Our results also show a detrimental relation between skipping breakfast and eating late in the day and children’s body weight. Considering all daily eating occasions, a higher proportion of energy and macronutrient intake at the main meals and a lower proportion during the afternoon and evening seems to be more beneficial for children’s weight. These results emphasize the important role of daily food intake rhythm on excessive weight gain in childhood.