Current estimates of methane emissions from high latitude wetlands have significant intermodel variations, one reason for which may be internal atmospheric circulation variability. This paper analyzes the impact of internal atmospheric variability on variations in methane emissions from the Hudson Bay Lowland (HBL) area. The ensemble of numerical experiments with a joint model of the methane cycle and heat and moisture transport in soil was performed. An ensemble of 45 realizations of the multi-year data of meteorological variables at the land surface, calculated by the ECHAM5 for different initial and identical boundary conditions for a 34-year period (from 1.01.1979 to 31.12.2012) was specified as space-distributed input data. Necessary physical characteristics of the soil were calculated in the module of heat and moisture transport, supplemented with an interactive scheme for calculating the area of the model cell occupied by the wetlands. Wetlands are estimated to occupy 8–20 % (with 11.4 % ensemble mean) of HBL region area. The ensemble average of annual emissions for HBL over the estimated period equals 6.1 TgCH4/yr with – 0.1 TgCH4/yr trend. The obtained uncertainty associated with climate noise equals 32 % for average annual emissions, and 31–38 % for individual months. It is shown that a significant contribution to the high uncertainty of methane emissions is made by the climatically determined variability of the wetland area.