Net ecosystem exchange of carbon was measured using eddy covariance for four growing seasons at a subarctic hummocky fen in northern Manitoba, Canada. Over a 115 day measurement period each year, cumulative net ecosystem exchange of carbon ranged from a gain of 49 g C m−2 to a loss of 16 g C m−2 with a mean loss of 6 g C m−2 from the fen, with an uncertainty of about ±34 g C m−2. Ecosystem respiration decreased with higher water tables (r2 = 0.3), especially in one summer when flooding occurred to 0.12 m above the peat surface. Additional methane emissions previously documented for the site of 4–5.7 g C m−2 year−1 added to the carbon loss. Carbon loss was measured from this same fen in the 1990s and it is likely that the carbon gain (peat accumulation) during past centuries has not continued in recent decades. Scaling to annual greenhouse gas emissions as a 100 year global warming potential showed that this fen is currently a source of 192–490 g CO2-equivalents m−2 year−1 based on both carbon dioxide and methane flux measurements, indicating that peat is decomposing.