AbstractFirst‐order streams flowing through peatlands receive, carry and transform large amounts of organic carbon, methane (CH4) and carbon dioxide (CO2) but remain poorly documented. The objectives of this study were to (a) identify the origins of CO2 and CH4 (thereafter C‐GHG for carbon greenhouse gases) in a peatland headwater stream, (b) determine the environmental factors driving C‐GHG export and emissions, and (c) quantify C‐GHG losses from this system and discuss its implications. Data were collected from eight sampling sites along a 3 km boreal peatland headwater stream (Eastern Canada) over the growing seasons 2019 and 2020. The studied stream was oversaturated in pCO2 [min: 2,044; max: 23,306 μatm] and pCH4 [14; 17,614 μatm]. A mass balance model showed that ∼81% of in‐stream CO2 originated from porewater seepage while the remaining 17% and 2% originated from in‐stream productivity and methane oxidation, respectively. Porewater seepage was concluded to be the primary source of CH4. Seasonal dissolved C‐GHG concentrations were negatively correlated with the peatland water table depth, suggesting an active release of carbon‐rich peat porewater during the base flow. Nevertheless, greater C‐GHG losses occurred during stormflow periods which acted as pulses with most of the C‐GHG being shunted downstream. The sum of C‐GHG export and emissions at our site was 8.08 gC m−2 y−1 with 86% being released to the atmosphere and 14% being exported downstream. Our study demonstrates that peatland headwater streams act as large sources of C‐GHG and that precipitation events and topography control the magnitude of the fluxes.