Manure storage tanks and animals in barns are important agricultural sources of methane. To examine the possibility of using an inverse dispersion technique based on a backward Lagrangian Stochastic (bLS) model to quantify methane (CH4) emissions from multiple on-farm sources, a series of tests were carried out with four possible source configurations and three controlled area sources. The simulated configurations were: (C1) three spatially separate ground-level sources, (C2) three spatially separate sources with wind-flow disturbance, (C3) three adjacent ground-level sources to simulate a group of adjacent sources with different emission rates, and (C4) a configuration with a ground level and two elevated sources. For multiple ground-level sources without flow obstructions (C1 and C3), we can use the condition number (K, the ratio of the uncertainty in the calculated emission rate to the uncertainty in the predicted ratio of concentration to emission rate) to evaluate the applicability of this inverse dispersion technique and a preliminary threshold of K <10 is recommended. For multiple sources with wind disturbance (C2) or an even more complex configuration including ground level and elevated sources (C4), a low kappa is not sufficient to provide reasonable discrete and total emission rates. The effect of flow obstructions can be neglected as long as the distance between the source and the measurement location is greater than approximately 10 times the height of the flow obstructions. This study shows that the bLS model has the potential to provide accurate discrete emission rates from multiple on-farm emissions of gases provided that certain conditions are met.