Peatlands are characterized by their large carbon (C) storage capacity and represent important C sinks globally. In southern Chile, young peatlands (few centuries old) have originated due to clearcutting or fire at forest sites with high precipitation on poorly drained soils. These novel ecosystems are called anthropogenic peatlands here. Their role in the regional C cycle remains largely unknown. Here, we present 18 months of eddy covariance measurements of net ecosystem exchange (NEE) of carbon dioxide (CO2) in an anthropogenic peatland in northern Chiloé Island, part of which is kept undisturbed for 30–40 years, by excluding human uses, and another section of the same peatland that has been disturbed by cattle grazing and Sphagnum moss extraction. Gross primary productivity (GPP) and ecosystem respiration (Reco) were modeled from NEE, based on measured photosynthetically active radiation and air temperature, separately for each section of the peatland. Uncertainties of the annual flux estimates were assessed from the variability of modelled fluxes induced by applying different time-windows for model development between 10 and 20 days. The undisturbed area of the peatland was on average (± SD) a larger net CO2 sink (NEE = − 135 ± 267 g CO2 m−2 year−1) than the disturbed area (NEE = − 33 ± 111 g CO2 m−2 year−1). These NEE CO2 balances are small even though GPP and Reco were larger compared with other peatlands. Reco had a direct relationship with water table depth (from soil surface) and a negative relationship with soil water fraction. Our results show that the disturbance by moss extraction and cattle grazing is likely to reduce the CO2 sink function of many anthropogenic and natural peatlands on Chiloé Island, which are subjected to the same impacts.