Peatlands store ~30% of global soil organic carbon (SOC) and are frequently carbon dioxide (CO2) sinks, while also being sources of methane (CH4) due to anaerobic decomposition under waterlogged soil conditions. Hence, the role of peatlands in the radiative forcing of the Earth’s atmospheric system and their impact on the global climate system is complex. This study presents the first long-term direct flux measurements of land-atmosphere CO2 and CH4 exchange at a temperate lowland fen peatland in East Anglia, UK. The dynamics and magnitude of CO2, H2O, CH4 and energy fluxes were quantified using the eddy covariance (EC) technique at two sites: a former-arable regenerating site (Baker’s Fen, BF) and a semi-natural fen (Sedge Fen, SF) at Wicken Fen NNR. This allowed investigation and comparison of ecosystem responses to climate variability and restoration. EC measurements at BF covered three annual cycles (2013 - 2015), and at SF two and a half cycles (August 2013 - December 2015). BF acted as a net CO2 source in all years, emitting 161.03±12.51, 83.61±11.53 and 98.39±13.31 g CO2-C m-2yr-1 in 2013, 2014 and 2015, respectively; it was a net CH4 source of 6.067±0.096 g CH4-C m-2yr-1 in 2013 and 2.009±0.087 g CH4-C m-2yr-1 in 2015, and of 2.845±0.103 g CH4-C m-2 (8th April - 31st December 2014). The annual carbon balance for BF was lower than average carbon losses from arable fens, indicating that restoration can achieve net carbon emissions reduction. SF was also a net CO2 source of 297.59±9.16 g CO2-C m-2 (1st August - 31st December 2013), and a large net CO2 sink of -356.86±49.13 g CO2-C m-2yr-1 in 2014 and of -243.78±15.25 g CO2-C m-2yr-1 in 2015. Large inter-annual variability in CO2 exchange at SF indicates sensitivity to climatic conditions, and highlights the need to maintain an appropriate water level height to prevent or reduce soil carbon losses to the atmosphere as CO2.