Abstract: British Columbia (BC), Canada is experiencing a severe mountain pine beetle (MPB) (Dendroctonus ponderosae) epidemic extending over an area of 135,000 km2. The widespread mortality of lodgepole pine (Pinus contorta var. latifolia) caused by the beetle has significant implications for BC’s timber supply and Canada’s carbon (C) budget. This study used the eddy-covariance technique to examine how the beetle is impacting the net ecosystem production (NEP) of two attacked lodgepole pine-dominated stands in the central interior of BC. MPB-06 is an 83-year-old stand that was first attacked in 2006. At the start of 2007 roughly 60% of the canopy had been attacked and by October 2008 only 21% of the trees remained healthy. MPB-03, a 110-year-old stand, had >95% pine canopy mortality as a result of a 2003 beetle attack, and also differed from MPB-06 in that it had a more developed secondary structure (consisting of tree seedlings and saplings and sub-canopy and canopy trees) that survived the beetle attack. Eddy-covariance measurements were also conducted in two stands near MPB-06 harvested in 2005 and 1997 (CC-05 and CC-97) for approximately three-week periods each during the 2007 growing season. MPB-06 had an annual NEP of 82 and 33 g C m2, while MPB-03 had an NEP of 56 and 4 g C m2 in 2007 and 2008, respectively. In the 2007 and 2008 growing seasons (May–September), MPB-06 was a sink of 12 and 52 g C m2, while MPB-03 was a sink of 17 and 68 g C m2, respectively. The productivity at MPB-06 resulted from an increase in photosynthesis by the remaining healthy trees and understory vegetation, while at MPB-03 the secondary structure and understory vegetation showed a strong capacity to sequester C due to an opening up of the stand as a result of canopy mortality. Average daily values of NEP during the measurement periods at CC-97 and CC-05 were 0.37 and 0.87 g C m2, respectively, showing that even 10 years following harvesting, these stands are likely to remain growing season C sources. That MPB-06 and MPB-03 were growing season C sinks suggests that deferring the harvest of stands with significant levels of secondary structure could prevent MPB-attacked forested areas from becoming C sources over extended periods.