The population of Timor deer (Rusa timorensis), an Indonesian endemic, continues to decline in its natural habitat, so captive breeding could become a source of individuals to bolster wild population. Support for captive breeding programs may be stronger if captive breeding also provided meat for human consumption. Thus, sustainable captive yields could be expected to support both conservation interests and food needs. The aim of this research is to evaluate the environmental impact, based on global warming potential (GWP), of two Timor deer breeding systems, that is, a farming system and a ranching system, in West Java, Indonesia. Life cycle assessment methodology was used for the evaluation to gain a cradle-to-gate perspective. The functional unit used was 1 kg of Timor deer live weight in captivity. The main result of the study indicated that the GWP per kg of Timor deer was estimated at 17.30 kgCO2eq (farming system) and 17.60 kgCO2eq (ranching system). The largest GWP in both systems was derived from cultivation activities and infrastructure development. In general, there is no significant difference in the GWP of the two breeding systems studied. This was due to the similar overall management adopted by the two breeding systems, especially the use of food types and infrastructure materials. Currently, the environmental dimension, especially the emissions from Timor deer breeding activities, is not a major concern, but in the future, breeding management should pay attention to the efficient use of the food and infrastructure to make it more environmentally friendly.