Technical Abstract: As a sector, agriculture is reported to be the third greatest contributor of methane (CH4) in the U.S., emitting one-quarter of total emissions. The primary sources of CH4 on a dairy farm are the animals and manure storage, with smaller contributions from field-applied manure, feces deposited by grazing animals, and manure on barn floors. The Integrated Farm System Model (IFSM) was expanded to include simulation of CH4 emissions from all farm sources using equations based upon previously published relationships and experimental data. This new CH4 module incorporated the best available models that were consistent with our modeling objectives and with the current structure of IFSM. In simulating a representative 100-cow dairy farm in Pennsylvania, the model predicted a total average annual emission of 20 Mg CH4. This included an average annual emission of 135 kg CH4 per cow from the Holstein herd and an average annual emission of 5.4 kg CH4 per m3 of stored manure, which were very similar to previously reported emissions. To illustrate the use of the whole-farm model, two potential methane reduction strategies were evaluated. Farm simulations showed that increasing the use of forage (corn silage) in animal diets increased CH4 emission by 17% with little impact on the global warming potential of net farm emissions of all greenhouse gases. Using a manure storage cover and burning the captured biogas reduced farm emission of CH4 by 30% with a 22% reduction in the global warming potential of the total farm emission of greenhouse gases. With the incorporation of this CH4 module, IFSM provides a tool for simulating whole-farm emissions of CH4 and evaluating the overall impact of management scenarios used to reduce emissions.