Fire and harvesting are major forest renewal processes in the Canadian boreal forest. The eddy covariance method was used to compare ecosystem fluxes of carbon dioxide between harvested and burned boreal forest sites in Saskatchewan, Canada. The harvest chronosequence had sites harvested in 2002 (HJP02), 1994 (HJP94) and 1975 (HJP75), whereas the fire chronosequence sites were burned in 1998 (F98), 1989 (F89), 1977 (F77) and 1929 (OJP). All sites were dominated by jack pine prior to the disturbance. During 2004 and 2005, net ecosystem production showed an average carbon gain (g C m−2 year−1) at F89 = 84, HJP75 = 80, HJP94 = 14 and OJP = 20. The other sites lost carbon (g C m−2 year−1) at HJP02 = −139, F98 = −20, and F77 = −58. Gross ecosystem production (GEP), ecosystem respiration (Re) and evapotranspiration tended to be greater at the burned sites than the harvested sites. The F89 and F77 sites had the strongest response of GEP to photosynthetically active radiation, and the strongest response of Re to soil temperature at the 2-cm depth. HJP02 had the weakest responses, followed by HJP94. This apparent greater ecosystem activity at the burned sites is likely caused by local differences in soil moisture and nutrients, differences in vegetation development, and differences in the decomposition of coarse woody debris.