While increasing methane emissions from thawing permafrost are anticipated to be a major climate feedback, no observational evidence for such an increase has previously been documented in the literature. Here we report a trend of increasing methane emissions for the early summer months of June and July at a permafrost site in the Lena River Delta, on the basis of the longest set of eddy covariance methane flux data in the Arctic. Along with a strong air temperature rise of 0.3 ± 0.1 °C yr−1 in June, which corresponds to an earlier warming of 11 d, the methane emissions in June and July have increased by roughly 1.9 ± 0.7% yr−1 since 2004. Although the tundra’s maximum source strength in August has not yet changed, this increase in early summer methane emissions shows that atmospheric warming has begun to considerably affect the methane flux dynamics of permafrost-affected ecosystems in the Arctic.