The present study has investigated how the Greenhouse gases like CO2 and H2O vapour are exchanged between biosphere and atmosphere for the first time at an eastern Himalayan site in India. The study was carried out over a high altitude (2286 m asl) evergreen coniferous forest (27.04°N, 88.08°E) where we measured the fluxes of CO2, H2O vapour along with the sensible and latent energy using eddy covariance method both above (38 m) and within (8 m) the canopy, soil-CO2 flux and the vertical profile of CO2 during spring (March–April) in 2015. The mean eddy flux of CO2 above the canopy was –2.8 ± 6.5 µmol m–2 s–1 whereas that within the canopy was 0.6 ± 0.4 µmol m–2 s–1. The mean flux of H2O vapour above the canopy (1.5 ± 1.8 mmol m–2 s–1) was three times higher than within the canopy (0.5 ± 0.6 mmol m–2 s–1). The mean flux of CO2 emitted from the soil surface was 1.6 ± 0.1 µmol m–2 s–1. The diurnal variation showed high sequestration of CO2 during daytime when the negative flux increased to larger than –10 µmol m–2 s–1. We observed that precipitation significantly enhanced CO2 sequestration (by ~four folds) as well as H2O vapour emissions (by ~three folds) by the tall canopies. Overall, during the entire study period the net ecosystem exchange (NEE) was –656.5 g CO2 m–2 suggesting that the evergreen coniferous forest at eastern Himalaya acts as a net sink of CO2 during spring. This would enable us to estimate the sequestration of anthropogenic carbon emission by the eastern Himalayan forest ecosystem and contribute to the national greenhouse gases inventory.