| Summary: | This study investigates the input–output energy-flow patterns and CO<sub>2</sub> emissions from the wheat–rice crop rotation system. In this regard, an arid region of Punjab, Pakistan was selected as the study area, comprising 4150 km<sup>2</sup>. Farmers were interviewed to collect data and information on input/output sources during the 2020 work season. The total energy from these sources was calculated using appropriate energy equivalents. Three energy indices, including energy use efficiency (<i>η<sub>e</sub></i>), energy productivity (<i>η<sub>p</sub></i>), and net energy (<i>ρ</i>), were defined and calculated to investigate overall energy efficiency. Moreover, the data envelopment analysis (DEA) technique was used to optimize the input energy in wheat and rice production. Finally, CO<sub>2</sub> emissions was calculated using emissions equivalents from peer-reviewed published literature. Results showed that the average total energy consumption in rice production was twice the energy consumed in wheat production. However, the values of <i>η<sub>e</sub></i>, <i>η<sub>p</sub></i>, and <i>ρ</i> were higher in wheat production and calculated as 5.68, 202.3 kg/GJ, and 100.12 GJ/ha, respectively. The DEA showed the highest reduction potential in machinery energy for both crops, calculated as −42.97% in rice production and −17.48% in wheat production. The highest CO<sub>2</sub> emissions were found in rice production and calculated as 1762.5 kg-CO<sub>2</sub>/ha. Our conclusion indicates that energy consumption and CO<sub>2</sub> emissions from wheat–rice cropping systems can be minimized using optimized energy inputs.
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