In an effort to bolster confidence and protect the nation the U.S. government through agencies like the Department of Homeland Security is identifying vulnerabilities and evolving strategies for protection. Agricultural food supply is one identified vulnerable area, and animal disease defense is one of the major concerns there under. Should an outbreak of animal disease occur, it is likely to have a mass slaughter and disposal of animal carcasses. The current existing policy, mainly including slaughter policy and strict movement bans, may be not sufficient to control disease spread at reasonable cost. We address the issue modeling vaccination as a supporting strategy with later slaughter of animals and argue that vaccination can decrease slaughter and disposal cost in the case of emergency. Our results show that (a) Vaccination gains time to slow down the flow of slaughter, thereafter the disposal operation of animal carcasses. By smoothing slaughter/disposal flow, vaccination likely decreases slaughter and disposal cost; (b) Vaccination likely reduce the total amount of slaughter and disposal of animals mainly because vaccinated animals shed less and disease spread slower; and (c) Vaccination becomes more valuable in reducing slaughter and disposal costs when the marginal cost of vaccination falls, the even size of disease outbreak is larger, the disease is more contagious and spreads faster, and/or vaccines are more effective in controlling disease spread.