Abstract The Syrian civil war caused a near total collapse of its health and veterinary infrastructure, affecting vaccinations, quarantine and border control. While outbreaks of zoonoses—diseases transmissible between animals and humans—in neighbouring countries are attributed to irregular cross-border movements, little remains known about the impact of conflict and displacement on livestock, and zoonotic disease risks in refugee and host populations. This case study investigates the role of livestock and zoonotic disease dynamics in the Syrian refugee context in Jordan, to inform policies and procedures for better inclusion of livestock in refugee responses. Key informant interviews were conducted with humanitarian, animal and public health experts, and household interviews with Jordanian and Syrian livestock keepers in Mafraq Governorate. Respondents attributed zoonotic disease outbreaks to cross-border smuggling of livestock, with no reports of refugees bringing animals into Jordan. While Syrian respondents diversify their livelihoods through animal husbandry, high-level political and practical barriers affect refugees’ access to livestock assistance, increasing zoonotic disease risks. To support animal and human health, stakeholders need to address structural inequalities through inclusive policies and support to both refugees and host populations.