For the first time, the exchange of greenhouse gases, such as CO2 and H2O vapour, between the biosphere and the atmosphere at an eastern Himalayan site in India has been investigated. This 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 and H2O vapour along with the sensible and latent energy using the eddy covariance method both above (38 m) and within (8 m) the canopy, the 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 it was 0.6 ± 0.4 µmol m–2 s–1 within the canopy. 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 beyond –10 µmol m–2 s–1. We observed that precipitation significantly enhanced CO2 sequestration (by approximately fourfold) as well as H2O vapour emissions (by approximately threefold) 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 in the eastern Himalaya acts as a net sink of CO2 during spring. Therefore, we can estimate the sequestration of anthropogenic carbon emission by the eastern Himalayan forest ecosystem, improving the national greenhouse gas inventory.