ABSTRACTRewetting is considered a strategy for mitigating carbon dioxide (CO2) emissions from drained peatlands, with associated climate benefits often derived by applying emission factors (EFs). However, data from rewetted sites are lacking, particularly for boreal peatland forests established on drained nutrient‐poor fens. Instead, their EFs have been developed primarily based on data from natural mires, implying similar carbon (C) cycles. In this study, we integrated eddy covariance measurements of ecosystem CO2 and methane (CH4) exchanges with dissolved C export estimates to compare the net ecosystem C balance (NECB) of a recently rewetted minerogenic peatland and two nearby undisturbed fen‐type mires in northern Sweden. We found that the rewetted peatland was an annual C source with a mean NECB of +77 ± 34 g C m−2 year−1 (±SD) over the initial 3 years following rewetting. In comparison, the mires were nearly C neutral or a C sink with their 3‐year mean NECB ranging between +11 and −34 g C m−2 year−1. The net CO2 emission of the rewetted peatland declined to about half by the third year coinciding with an increase in gross primary production. Annual CH4 emissions from the rewetted peatland steadily increased but remained at 32% and 49% in the first and third year, respectively, relative to the mires. We further noted differences in key environmental response functions of CO2 and CH4 fluxes between the rewetted and natural peatlands. Relative to the mires, the dissolved C loss was significantly greater in the rewetted peatland during the first year, but similar in subsequent years. Thus, our study demonstrates that the C balance of a recently rewetted minerogenic peatland may not immediately resemble that of natural mires. This further highlights the need for separate and dynamic EFs to improve estimates of the short‐term climate benefit of rewetting measures.