We evaluated the utility of Ecosim for exploring interactions between cetacean predators, their prey, and fisheries. We formulated six Ecosim parameterizations, representing alternative hypotheses of feeding interactions (functional response) between cetaceans and their main fish prey, and examined differences in the predicted responses to simulated harvesting regimes for minke whales and their prey. Regardless of the type of function response formulated, intense fishing on the main fish prey of minke whales had a longer-lasting negative impact on minke whales than when minke whale biomass was removed directly by harvesting. Consumption rate, biomass, feeding time and mortality of minke whales were all sensitive to the type of functional response specified. Inclusion of “handling time” limited minke whales consumption at high prey densities and predicted higher consumption at low prey densities; features characteristic of a type II functional response. Predicted decline and recovery rates of minke whales were slower than when consumption rates were not limited. Addition of “foraging time” adjustments resulted in more conservative estimates of decline and recovery. However, when “other mortality” was linked to time spent foraging, exposure to higher mortality at low prey densities, and reduced mortality at high prey densities resulted in dramatic differences in predicted biomass trajectory. Sensitivity to the “other mortality” assumption is important for cetaceans whose predation mortality is only a small proportion of total mortality. Differences in the feeding and biomass dynamics were also observed when prey availability to predators was represented by changes in prey vulnerability, confirming earlier reports that Ecosim predictions are sensitive to this parameter.