Childhood obesity estimates are steadily increasing worldwide. There is strong evidence that overweight children before puberty maintain this nutritional status for life. This study aimed to estimate the prevalence and incidence rates of overweight and obesity among children recruited as part of the Generation XXI birth cohort. Of the 8036 included children, 5497, 5397 and 4956 of them had follow-up measurements at 4, 7 and 10 years of age, respectively. The chi-square test, Student's t-test, and survival curves were estimated according to sex. The prevalence of overweight remained stable at 4 and 7 years of age (22.0% and 22.1%, respectively) and slightly increased at age 10 (26.1%). Conversely, obesity prevalence increased with age (from 10.6 to 16.8%). Overweight was more prevalent in girls at all follow-ups, whilst obesity was similar between sexes at ages 4 and 7 (p = 0.050 and p = 0.218, respectively) but was more prevalent in boys at age 10 (p = 0.017). The incidence of obesity between 4 and 7 years of age was 11.4/1000 person-years, decreasing to 3.2/1000 person-years between 7 and 10 years of age. Our results reveal a high prevalence/incidence of obesity mainly among 4 and 7-year-old children, heightening the need for interventions at early ages to effectively curb childhood obesity in Portugal.