In modern agriculture, reducing the carbon footprint and emission of greenhouse gases with greater energy efficiency are major issues for achieving the sustainability of agricultural production systems. To address this issue, a long-term field experiment was established from 2001 through 2016 with two contrasting tillage practices (ZT: zero tillage; CT: conventional tillage) and four irrigation schedules {I-1: pre-sowing (PS), I-2: PS + crown root initiation (CRI), I-3: PS + CRI + panicle initiation (PI)/flowering (FL), and I-4: PS + CRI + PI/FL + grain filling (GF)}. The grain yield of rice, wheat and the rice–wheat system was increased significantly by 23.6, 39.5 and 32.8%, respectively, with irrigation at four stages (I-4) compared to a single stage (I-1). Energy appraisal results exhibited that 17.2% higher energy was consumed under CT as compared to ZT (25,894 MJ Ha−1). Fertilizer application consumed the highest energy (46.5–54.5%), followed by irrigation (8.83–19.5%), and the lowest energy consumption was associated with winnowing, packing and transport (2.07–2.43%) operations. The total energy output of the rice–wheat system did not change significantly among contrast tillage, but higher energy was obtained under CT (214,603 MJ ha−1) as compared to ZT (209,728 MJ Ha−1). ZT practice improved the energy use efficiency (EUE), energy productivity (Ep) and energy profitability (Eprof) by 16.6, 21.0 and 16.6%, respectively, over CT. The EUE, SE (specific energy), Ep, net energy return (NER) and Eprof were enhanced by 17.1, 16.6, 21.0, 36.5 and 20.6%, respectively, with irrigation at four stages (I-4) compared to a single stage (I-1). Zero tillage plots reflected a 8.24% higher carbon use efficiency (CUE) and a 9.0% lower carbon footprint than CT plots. Among irrigation schedules, application of I-4 showed a 8.13% higher CUE and a 9.0% lower carbon footprint over single irrigation (I-1). This investigation indicated that ZT with irrigation at four stages (I-4) was the most sustainable option for improving the EUE and CUE with minimal GHGs emissions from the rice–wheat cropping system of Indian mid-Himalayan regions.