Abstract Background Over the last decades, immigration have increased markedly in Sweden. Educational achievement is essential for successful integration; however, second generation immigrants have been shown to lag behind. There is a complex intertwinement between educational attainment and health outcomes. Thus, schooling is crucial in terms of integration but also from a public health perspective. We aim to compare school performance and health in children of immigrant parents and children of parents born in Sweden. Methods In this population-based cohort study, 1723 children were followed from birth to age 20. Of these 246 (14.3%) had at least one parent born abroad. Logistic regression was performed controlling for gender, language spoken at home and sociodemographic data obtained at 3 months, 3-, 12- and 20 years. Outcome measures were school performance at age 12 (n = 984), grades from compulsory and upper secondary school (n = 1668) and register data on psychiatric diagnoses (n = 737). Self-response questionnaires on general health, long term health problems and psychiatric conditions were administered at age 20 (n = 731). Results There were no differences in reading (p = 0.676) or mathematics (p = 0.324) at age 12, eligibility to upper secondary school (p = 0.298) or university (p = 0.232) between second generation immigrants and children of native-born parents. No differences in frequency of psychiatric diagnoses (p = 0.112), presence of long-term health problems (p = 0.267) or self-reported health (p = 0.595) were shown. Conclusions The results indicate that young adults born in Sweden in the middle of the 1990’s with immigrant parents perform similarly in school compared to children of parents born in Sweden. They are not at increased risk for mental illness, long-term health conditions and report their general health equivalently to children of native-born. The comprehensive school system and child health programs used in Sweden are likely important factors to promote education and health. Key messages • In a birth-cohort of children followed into early adulthood, no difference in educational achievement or health was shown between second generation immigrants and children of parents born in Sweden. • International comparative studies are needed to highlight the importance of underlying structural and socio-cultural factors.