The apparent kinetic isotope effect (ɛA) inferred from measurements of methane (CH4) and δ13CH4 in the extratropical Southern Hemisphere (ETSH) is significantly larger than expected if the sink were caused by hydroxyl radical (OH•) alone. If the OH• sink were the primary driver for the observed seasonal cycles in CH4 and δ13CH4 in the ETSH, published laboratory data suggest an ɛA of the order −3.9‰. However, a value of the order −11‰ has been inferred from measurements in the background troposphere. Atomic chlorine (Cl•) in the marine boundary layer (MBL) could explain the difference, but an alternative hypothesis is that the large ɛA in the ETSH is due to seasonally varying CH4 emissions. We test this by sequentially omitting or doubling CH4 emissions from each seasonally varying source in the UMeth model (Unified Model with Methane) and evaluating the corresponding effects on ɛA at Baring Head (41.40°S). If only the OH• sink is included, the maximum change in ɛA is about 1.7‰. When both OH• and a mean Cl• concentration of 18 × 103 atoms cm−3 in the MBL are included, the maximum change in ɛA is about 1.1‰. For realistic changes in the CH4 sources over a few years (∼10% of the simulated changes), we estimate that changes in ɛA are of the same order as the uncertainties in the derivation of ɛA from time series of CH4 and δ13CH4 over a comparable period. We conclude that realistic changes in seasonally varying CH4 sources do not significantly affect ɛA or previously derived estimates of the MBL Cl• sink using ɛA.