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There is evidence of learning loss due to the COVID-19 pandemic, but there is no related information for Mexico. The objective of the study is to estimate learning loss in reading and numeracy in Mexico. We compared the results of two household surveys conducted in 2019 and 2021. We interviewed 3161 children between 10 and 15 years. We estimated a learning loss according with SES in a range from 0.34–0.45 SD in reading and 0.62–0.82 SD in mathematics by COVID-19 pandemic, and an increase in learning poverty in a range of 25.7%–15.4% in reading and 29.8%–28.8% in numeracy. Gaps in fundamental learning by gender and SES increased. There is an urgent need develop a clear strategy to perform personalized diagnoses and implement remedial courses to address learning loss. • Prolonged school closures have increased learning loss around the world. • In Mexico, we estimated a learning loss in a range from 0.34 to.045 SD in reading and 0.62-0.82 SD in numeracy. • According to SES, we found an increase in learning poverty in a range of 25.7%–15.4% in reading and 29.8%–28.8% in numeracy. • Gaps in fundamental learning by gender and SES increased. • We discussed the need to establish a strategy to address these lags through remedial courses that teach at the right level.