Arctic and boreal permafrost ecosystems in Eastern Siberia, considered crucial to the climate system and global carbon cycle, are particularly vulnerable to climate change. This study investigates carbon dioxide (CO2) exchange fluxes over northeastern Siberia from 2013 to 2015 in a taiga–tundra boundary ecosystem for which such measurements are scarce. The growing season (May–September) net CO2 exchange flux (NEE) was −39.4 (−60.1 to −20.2) gCm−2, with ecosystem respiration (RE) = 306.2 (288.1–317.9) gCm−2 and gross primary production (GPP) = −345.5 (−372.5 to −317.7) gCm−2. Microclimatic factors determining these CO2 exchange fluxes change seasonally. These fluxes are significantly affected by the timing of the onset of C uptake, which is reflected by changes in the soil temperature in spring and early summer, following which fluxes respond well to the photosynthetic photon flux density, especially for NEE. These CO2 exchange fluxes at the northeastern Siberian taiga–tundra boundary ecosystem are significantly smaller than those previously reported at southern-taiga forest sites. Spring snow meltwater-rich soil moisture conditions render southern-taiga sites as stronger CO2 sinks in June than taiga–tundra boundary ecosystem, which may be largely responsible for the pronounced north–south gradient in growing season NEE.