The contribution from northern high latitude wetlands are a major uncertainty in the atmospheric methane (CH4) budget throughout the Holocene. We reconstructed CH4 emissions from northern peatlands from 13,000 BP to present using an empirical model based on observations of peat initiation (>3600 dates), peatland type (>250 peat cores), and observed CH4 emissions in order to explore the effects of changes in wetland type on CH4 emissions over the end of the late glacial and the Holocene. Fen area increased steadily before 8000 BP as fens formed in major wetland complexes. After 8000 BP, new fen formation continued but widespread peatland succession (to bogs) and permafrost aggradation occurred. Reconstructed CH4 emissions from peatlands increased rapidly between 10,600 BP and 6900 BP due to fen formation and expansion. Emissions stabilized after 5000 BP at 42 ± 25 Tg CH4 y−1 as high-emitting fens transitioned to lower-emitting bogs and permafrost peatlands. Widespread permafrost formation in northern peatlands after 1000 BP decreased CH4 emissions by 20%–34 ± 21 Tg y−1 by the present day and suggests peatland CH4 emissions will increase with permafrost thaw.