Managing the Grey-headed Flying-fox Pteropus poliocephalus as a species vulnerable to extinction in New South Wales (NSW) is complicated by contentious issues arising from flying-foxes feeding on commercial fruit and roosting in populated areas. Two decades on from their threatened species listing in 2001, there have been major developments in managing these issues. The NSW Flying-fox Consultative Committee was formed in 2001 with representation of a range of stakeholder groups. A transition towards non-lethal means of protecting horticultural crops from flying-fox damage was supported by government programs that encouraged the uptake of exclusion netting in orchards. Cull limits and restrictions on licences to shoot flying-foxes on horticultural land were steps to the phasing out of legal shooting of flying-foxes. The need to address community concerns about flying-fox camps in populated areas led to the development of the Flying-fox Camp Management Policy and funds to support land managers to implement policy actions. Dispersing camps has been largely ineffective in the long-term, placing the emphasis on managing camps in-situ. This has involved physical buffers between flying-foxes and human settlements and subsidising equipment and services for residents to self-mitigate impacts from flying-foxes. However, community sentiments continue to be influenced by the difficulties experienced by affected communities, perceived disease risks from flying-foxes, frustrations with there being no immediately effective solutions and the portrayal of flying-foxes and associated issues in the media. To address these issues, there has been considerable effort to engage communities to promote the ecological importance of flying-foxes, reduce misconceptions about disease transmission risks, and promote precautionary measures for reducing these risks; as well as research on mitigation measures for flying-fox impacts. To conserve the Grey-headed Flying-fox while addressing ongoing contentious issues impacting horticulturalists and communities, there needs to be investment into long-term solutions, such as public education, social research and conserving and restoring habitat in less populated areas. There is a need for cross-jurisdictional collaboration on managing the Grey-headed Flying-fox since this threatened species is mobile and not constrained to jurisdictional borders.