The northern wetlands are one of the major sources of methane into the atmosphere. We measured annual methane emission from a boreal minerotrophic fen, Siikaneva, by the eddy covariance method. The average wintertime emissions were below 1 mg m−2 h−1, and the summertime emissions about 3.5 mg m−2 h−1. The water table depth did have any clear effect on methane emissions. During most of the year the emission depended on the temperature of peat below the water table. However, during the high and late summer the emission was independent on peat temperature as well. No diurnal cycle of methane flux was found. The total annual emission from the Siikaneva site was 12.6 g m−2. The emissions of the snow free period contributed 91% to the annual emission. The emission pulse during the snow melting period was clearly detectable but of minor importance adding only less than 3% to the annual emission. Over 20% of the carbon assimilated during the year as carbon dioxide was emitted as methane. Thus methane emission is an important component of the carbon balance of the Siikaneva fen. This indicates need of taking methane into account when studying carbon balances of northern fen ecosystems.