The quantification of carbon (C) footprints in crop production is important to underpin the greenhouse gas (GHG) mitigation options. The present study aims at accounting C footprints of high-input intensive rice (Oryza sativa L.)-wheat (Triticum aestivum L.) cropping system in north-western India, and the optimization of the amount of input-induced carbon equivalent (CE) emissions that could be reduced at a current level of economic output. We quantified the C footprints related to different agri-inputs and agri-machinery employed for different farm operations based on life cycle assessment (LCA) approach. The data were collected for 80 farms (40 each under rice and wheat cultivation), which were used to estimate CE emissions based on specific emission coefficients. This study quantified the CE emissions and the amount of carbon dioxide (CO2) sequestered in soils to estimate GHG mitigation potential of a rice-wheat cropping system. We employed slack-based measure (SBM) data envelopment analysis (DEA) to elucidate the efficient and inefficient farms (i.e., decision-making units (DMUs)) under rice-wheat cropping system. A multiple linear regression output predictive model was used to predict and compare the predicted vs. actually measured crop yield. The input-induced total CE emissions (CET) in rice, wheat, and rice-wheat cropping system were 2438.3 +/- 73.5, 1682.1 +/- 33.1, and 4120.2 +/- 88.6 kg CO2e ha(-1), respectively. Of these emissions, the amount of CO2 sequestered in soils under rice, wheat, and rice-wheat cropping system comprised similar to 10.0%, 8.0%, and 9.2%, respectively. Fertilizer-N, fertilizer-P2O5, and fertilizer-K2O application accounted for 95-98%, 1.6-5.1%, and 0.3-0.8% of total fertilizer-related carbon equivalent emission (CEF). About 71% of CE emissions related to electricity consumption (CEE) in the rice-wheat system were ascribed to irrigation in rice cultivation. The SBM-DEA approach elucidated 24 DMUs (60% of total DMUs) under rice and 18 DMUs (45% of total DMUs) under wheat cultivation as efficient with technical efficiency (TE) score = 1.00. On average, inefficient rice and wheat DMUs respectively had similar to 18.3% and 7.6% higher CET than the efficient DMUs. More specifically, the inefficient DMUs mainly had significantly higher electricity, chemical fertilizers, and diesel fuel-related CE emissions, compared with the efficient ones. These results revealed that up to similar to 57-63% CET emissions could be reduced in rice and wheat, if inefficient DMUs start following the management practices of efficient DMUs at their current yield level. The fitted regression model exhibited inverse relationship with rice and wheat yields and CE emissions, which revealed that DEA has optimized the input use at a level of current output level.