A secular trend in body height has been experienced in many nations and populations, hypothesized to be the result of better living conditions. Educational level has been shown to be closely associated with body height. This study examined the changes in body height and popliteal height in a group of adult Chilean male workers by age cohort and the relationship of these with educational level. The body heights and popliteal heights of 1404 male workers from the Valparaíso and Metropolitan regions of Chile were measured in 2016. The sample was grouped by level of education (primary, secondary, technical and university) and age (21–30, 31–40 and 41–50 years). Robust ANOVA and post-hoc analyses using a one-step modified M-estimation of location were conducted based on bootstrap resampling. Both body height and popliteal height increased from the older to the younger age cohort. The largest increase was from the 41–50 to the 21–30 group, with a 1.1% increase in body height and 1.7% increase in popliteal height. When educational level was introduced into the analysis there was a marked increase in both body height and popliteal height for each cohort, but only in primary- and secondary-educated workers. Despite showing an overall increase in body height and popliteal height, younger workers with the highest levels of education showed fewer differences between them than did older workers with less education. The differences were larger in the older than in the younger cohorts. Similarly, this trend was less clear in workers with higher levels of education (technical and university), probably because of a dilution effect caused by increased access to higher education by workers in the lower income quintiles.