Childhood obesity is a major international problem, and unhealthy eating habits remain widespread. Increasing the frequency of meals of nutritious food can help children to regulate their appetite and maintain a healthy weight. However, there is scarce prospective evidence on the relationship between the meal frequency and weight outcomes. Therefore, the objective of the present study was to determine the prospective association between the meal frequency, body mass index, and waist circumference in Spanish children. Additionally, we analyzed the impact of the meal frequency on the incidence of excessive weight and abdominal obesity. The study included 1400 children with a mean (SD) age of 10.1 (0.6) and an average follow-up of 15 months. Anthropometric measurements, including the body weight, height, and waist circumference, were measured by trained personnel, and children were asked about whether they usually had the following meals: breakfast, a mid-morning snack, lunch, an afternoon snack, and dinner. Multiple linear regression models revealed a significant (p < 0.05) inverse association between the meal frequency with a standardized BMI (zBMI) and the waist-to-height ratio (WHtR) after adjusting for sex, age, allocation to an intervention group, school, maternal education, physical activity, diet quality, and for the corresponding outcome variable at the baseline. Furthermore, the odds of developing abdominal obesity or excessive weight during the follow-up significantly decreased with an increase in the meal frequency after controlling for the same confounders. In conclusion, a higher meal frequency at the baseline was predictive for a lower zBMI, WHtR, and odds of the incidence of excessive weight and abdominal obesity.