This study documents differences in childhood IQ trajectories of Guatemala City children, aged 6–15 years and born 1961–1993, according to school attended, height-for-age Z-scores (HAZ) and over time (Flynn effect). IQ data come from the Universidad del Valle de Guatemala Longitudinal Study of Child and Adolescent Development. IQ was measured using standardised tests from the Otis-Lennon Mental Ability Test-series. A multilevel model was developed to describe 60,986 IQ observations (level 1), in 22,724 children (level 2), in five schools representing students of different socioeconomic status (SES) (level 3). Average IQ trajectories differed by school. The difference in average IQ at age 11 years between the students of high and low SES schools was 28.7 points. A one-unit increase in HAZ was associated with a 1.42 (0.72, 2.11) unit higher IQ if HAZ was <0, this association was stronger in public compared to private schools. Conversely, one unit increase in HAZ was only associated with a 0.3 (0.001, 0.5) unit higher IQ if HAZ was ≥0. With each birth year increase, IQ at age 11 years increased by 0.14 (95% CI 0.12, 0.16) units, although this Flynn effect attenuated slightly across adolescence. We found no evidence of secular change in the inequality in IQ trajectories (according to school or HAZ). Shorter children from disadvantaged schools in Guatemala City have lower IQ than their taller and wealthier peers, possibly reflecting the damaging effects of poor early life environments both for linear growth and cognitive development.