The study site, which is located near Summit Lake (54°13' 25'' N, 122°36' 53'' W) about 40 km north of Prince George BC, was first attacked in 2005. MPB-09 is a 70-year old stand that was partially harvested during February to March 2009, by removing the dead lodgepole pine trees and retaining the secondary structure consisting mainly of black spruce (Picea mariana), hybrid white spruce (Picea engelmannii x glauca) and subalpine fir trees (Abies lasiocarpa) with a canopy height of ~16 m. MPB-09C was harvested at the same time. NEP has been measured at MPB-09 since October 2009 using the eddy‐covariance technique with an ultrasonic anemometer (model CSAT3, Campbell Scientific Inc.) and an open‐path infrared gas analyzer (model LI-7500, LI-COR Inc.) mounted 26 m above the ground. Results for 2010 and 2011 are presented along with supplementary meteorological measurements and an energy balance closure analysis. The annual NEP at MPB-09 was -110 g C m-2 in 2010 and -10 g C m-2 in 2011. The increase of NEP in 2011 resulted from an increase in gross ecosystem photosynthesis from 2010 to 2011. During the growing season of 2010, NEP at MPB-09C was -132 g C m-2 compared to -18 g C m-2 at MPB-09, indicating the C loss at the clearcut was much higher than at the partially harvested stand. The study shows that secondary structure can play an important role in enhancing CO2 uptake of MPB-attacked stands and has important implications for forest management.