Background: This study aimed to examine the association between breakfast consumption and childhood weight status, in relation to various socioeconomic and lifestyle factors. Methods: A cross-sectional survey was conducted including 1,728 children aged 10–12 years and their parents, during the school years 2014–2016. Primary schools from five Greek counties (including the Athens metropolitan area) were randomly selected. Parental and child data were collected through self-administered, anonymous questionnaires. Children’s weight status was based on gender- and age-specific tables derived from the International Obesity Task Force body mass index cutoffs. Logistic regression was used to determine the association between frequency and type of breakfast consumption and children’s weight status. Results: The frequency of breakfast consumption was not associated with childhood overweight or obesity, even when other factors were included in the analysis like sex, age, physical activity, meals / day, family annual income, parental weight status, parental physical activity level, parental educational level and parental employment status. From the nine foods that were included only the consumption of bread or rusks and chocolate milk were found to have a negative association with childhood overweight or obesity (odds ratio: 0.51; 95% CI: 0.34, 0.79 and OR: 0.50; 95% CI: 0.28, 0.87, respectively). Conclusions: The result that frequency of breakfast consumption was not associated with children’s overweight / obesity may lead to a deeper investigation of the foods consumed during breakfast. Bread or rusks and chocolate milk seemed to have a protective effect; further nutritional analysis is needed to explore the potential mechanisms of this observation.