In the anticipated water scarcity and global warming scenario; it is imperative to identify suitable irrigation scheduling strategy in paddy fields for increasing water productivity and mitigating greenhouse gas (GHG) emissions. We conducted a two year (dry season of 2014 and 2015) field experiment for irrigation scheduling based on tensiometric measurement of soil water potential (SWP) in order to quantify temporal and seasonal variations in GHGs emissions and their trade off relationship at five levels of SWPs viz. SWP 1 (−20kPa), SWP 2 (−30kPa), SWP 3 (−40kPa), SWP 4 (−50kPa) and SWP 5 (−60kPa), in addition to the traditional practice of growing flooded rice (CF). Fluxes of methane (CH4) and nitrous oxide (N2O) during the growing period were measured using manual closed chamber-gas chromatograph and the carbon dioxide (CO2) flux was measured using an infrared CO2 analyzer. A significant decrease in seasonal cumulative CH4 emission (30–60.2%) was recorded at different SWPs as compared to CF. In contrast, emission of CO2 and N2O increased by 12.9–26.6% and 16.3–22.1% respectively at SWPs 1 and 2; conversely, a significant decrease in emissions of these gases were observed at higher SWPs (SWPs 3–5). Among different SWP treatments, irrigation scheduling at SWP 2 maintained yield at par with CF with water saving of 32.9–41.1% and reduced CH4 emission (43–44.1%). However, due to increase in CO2 and N2O emission at SWP 2, there was no significant reduction in global warming potential (GWP) as compared with CF. Among different rice growth stages GHGs emission were predominant during vegetative growth stage. Regression relationship of GHGs emission with key soil parameters was employed to predict seasonal emissions of GHGs from paddy field. The results of this study suggest that scheduling irrigation at SWP 2 can be an effective strategy in order to save water, maintain rice yield and mitigate CH4 emission from direct seeded paddy fields in eastern India, however further research is needed to identify suitable management strategy for reducing CO2 and N2O emissions at SWP 2 in order to reduce the GWP.