Background
Birth by caesarean section has been shown to alter the composition of the early infant gut microbiota and postulated to influence cognitive outcomes via the gut‐brain axis.

Aims
To determine whether birth by caesarean section is associated with secondary school educational achievement.

Methods
Whole‐population administrative data were used from anonymised individual level linkage of birth records to educational and health information from the New Zealand Integrated Data Infrastructure (IDI). Participants were 111 843 children born between 1 January 1996 and 31 December 1998 for whom mode of delivery information was available from International Classification of Diseases 9th edition codes in maternal records. The National Certificate of Educational Achievement (NCEA) is the main secondary school qualification undertaken by New Zealand students. Multivariable linear regression models were used to examine the association between mode of delivery and educational achievement. A family fixed effect analysis compared educational achievement outcomes in sibling pairs where one sibling was delivered by caesarean section and one delivered vaginally.

Results
After adjustment for potential confounders, there was no significant association between mode of delivery and achievement of university entrance (odds ratio = 0.98, 95% CI: 0.94‐1.02). NCEA percentile scores were lower in caesarean born infants (Estimate = −0.37, 95% CI: −0.69 to −0.06)). However, in the fixed effect sibling analysis caesarean section was no longer significantly associated with NCEA percentile scores.

Conclusions
We find that caesarean section is not related to educational outcomes, suggesting that even if the infant gut microbiota is altered in caesarean section, it does not appear to have a measurable impact on adolescent academic achievement.