Household chaos, which reflects the level of disorganisation and confusion that children experience in their family homes, is thought to precipitate the transmission of family background inequality in education. Here, we present a longitudinal, genetically informative study of the developmental interplay between household chaos and educational achievement, using data from the Twins Early Development Study (TEDS) that recruited families with twins born between 1994 and 1996 in England and Wales. Up to 7,591 pairs of twins completed the Confusion, Hubbub, and Order Scale (CHAOS), a state-of-the-art measure of household chaos, at the ages 9, 12, and 16 years, and also had their end-of-year school grades recorded. We observed small but consistent bidirectional negative effects between household chaos and educational achievement over time (i.e., cross-lagged paths) after controlling for both constructs’ stability and cross-sectional inter-correlations. Fitting biometric autoregressive cross-lagged twin models, we found that the cross-lagged paths from earlier household chaos onto later educational achievement could be attributed to shared environmental influences that were independent of family socioeconomic status (SES). The cross-lagged paths in the reverse direction, from earlier educational achievement to later household chaos, were entirely due to genetic factors after controlling for family SES. These findings suggest that household chaos contributes to the transmission of family background inequality in education during childhood and adolescence largely because of genetic and environmental confounding, rather than having causal effects.