Forests at northern high latitudes are experiencing climate-induced changes in growth and productivity, but our knowledge on the underlying mechanisms driving seasonal CO2 fluxes in northern boreal trees comes almost exclusively from ecosystem-level studies on evergreen conifers. In this study, we measured growing season whole-branch CO2 exchange in a deciduous tree species of the tundra-taiga ecotone, Mountain Birch (Betula pubescens ssp. czerepanovii (Orlova) Hamet-Ahti), at two locations in northern Fennoscandia: Abisko (Sweden) and Kevo (Finland). We identified strong seasonal and environmental controls on both photosynthesis and respiration by analysing the parameters of light response curves. Branch-level photosynthetic parameters showed a delayed response to temperature, and, at Kevo, they were well described by sigmoid functions of the state of acclimation (S). Temperature acclimation was slower (time constant, τ = 7 days) for maximum photosynthesis (βbr) than for quantum efficiency (αbr) (τ = 5 days). High temperature-independent values of the respiration parameter (γbr) during leaf and shoot expansion were consistent with associated higher growth respiration rates. The ratio γbr/βbr was positively related to temperature, a result consistent with substrate-induced variations in leaf respiration rates at the branch level. Differences in stand structure and within-site variation in the active period of C uptake determined the spatiotemporal patterns in net assimilation amongst branches. Growing season CO2 uptake of individual branches on a leaf area basis did not show a significant relationship with total incident photosynthetically active radiation, and did not differ across sites, averaging ca. 640 g CO2 m−2.