Agriculture is the largest sector of Pakistan’s economy, contributing almost 22% to the GDP and employing almost 45% of the total labor force. The two largest food crops, wheat and rice, contribute 3.1% and 1.4% to the GDP, respectively. The objective of this research was to calculate the energy return on investment (EROI) of these crops on a national scale from 1999 to 2009 to understand the size of various energy inputs and to discuss their contributions to the energy output. Energy inputs accounted for within the cropping systems included seed, fertilizer, pesticide, human labor, tractor diesel, irrigation pump electricity and diesel, the transport of fertilizer and pesticide, and the embodied energy of tractors and irrigation pumps. The largest per-hectare energy inputs to wheat were nitrogen fertilizer (52.6%), seed (17.9%), and tractor diesel (9.1%). For rice, the largest per-hectare energy inputs were nitrogen fertilizer (32%), tube well diesel (19.8%), and pesticide (17.6%). The EROI of wheat showed a gradual downward trend between 2000 and 2006 of 21.3%. The trend was erratic thereafter. Overall, it ranged from 2.7 to 3.4 with an average of 2.9 over the 11-year study period. The overall trend was fairly consistent compared to that of rice which ranged between 3.1 and 4.9, and averaged 3.9. Rice’s EROI dipped sharply in 2002, was erratic, and remained below four until 2007. It rose sharply after that. As energy inputs increased, wheat outputs increased, but rice outputs decreased slightly. Rice responded to inputs with greater output and an increase in EROI. The same was not true for wheat, which showed little change in EROI in the face of increasing inputs. This suggests that additional investments of energy in rice production are not improving yields but for wheat, these investments are still generating benefits. The analysis shows quantitatively how fossil energy is a key driver of the Pakistani agricultural system as it traces direct and indirect energy inputs to two major food crops.