Within the FLUXNET network of tower stations for performing long-term measurements of CO2 exchange between forest ecosystems and the atmosphere, most research has focused on mature forests that are strong carbon sinks. Nevertheless, it is just as valuable to quantify fluxes from recently disturbed forests so that we can recognize and predict the impact of disturbance on carbon fluxes. We measured carbon fluxes and microclimatic variables within a naturally regenerating, young (12–14 years of age) jack pine ecosystem in northern Michigan. During the months June to October of 2001–2003, this ecosystem exhibited a low net uptake of approximately 17.8–18.3 g C m−2 5 months−1. Soil respiration was independently measured and then modeled on the basis of soil temperature and soil moisture. Model estimates of soil respiration were 627, 583, and 681 g C m−2 5 months−1 from June to October in 2001, 2002, and 2003, respectively. Net ecosystem exchange (NEE) and soil respiration were inversely correlated in midsummer (r = −0.6, p = 0.001) during the period of lowest NEE (greatest uptake) and highest soil respiration rates. In the spring, NEE and soil respiration were positively correlated (r = 0.4, p = 0.01). During the fall, when soil temperatures remained fairly steady and air temperatures fluctuated, this coefficient between NEE and soil respiration declined to an average −0.25 (p = 0.2). Our results indicate that 12–14 years following disturbance this ecosystem displays a small net uptake during the June to October months but respiratory losses during the snow season (mid-October to April) could possibly counterbalance this carbon gain.