Boreal peatlands represent a globally important store of carbon, and disturbances such as wildfire can have a negative feedback to the climate. Understanding how carbon exchange and greenhouse gas (GHG) dynamics are impacted after a wildfire is important, especially as boreal peatlands may be vulnerable to changes in wildfire regime under a rapidly changing climate. However, given this vulnerability, there is very little in the literature on the impact such fires have on methane (CH4) emissions. This study investigated the effect of wildfire on CH4 emissions at a boreal fen near Fort McMurray, Alberta, Canada, that was partially burned by the Horse River Wildfire in 2016. We measured CH4 emissions and environmental variables (2017–2018) and CH4 production potential (2018) in two different microform types (hummocks and hollows) across a peat burn severity gradient (unburned (UB), moderately burned (MB), and severely burned (SB)). Results indicated a switch in the typical understanding of boreal peatland CH4 emissions. For example, emissions were significantly lower in the MB and SB hollows in both years compared to UB hollows. Interestingly, across the burned sites, hummocks had higher fluxes in 2017 than hollows at the MB and SB sites. We found typically higher emissions at the UB site where the water table was close to the surface. However, at the burned sites, no relationship was found between CH4 emissions and water table, even under similar hydrological conditions. There was also significantly higher CH4 production potential from the UB site than the burned sites. The reduction in CH4 emissions and production in the hollows at burned sites highlights the sensitivity of hollows to fire, removing labile organic material for potential methanogenesis. The previously demonstrated resistance of hummocks to fire also results in limited impact on CH4 emissions and likely faster recovery to pre-fire rates. Given the potential initial net cooling effect resulting from a reduction in CH4 emissions, it is important that the radiative effect of all GHGs following wildfire across peatlands is taken into account.