The Queensland Fruit Fly (QFF) — Bactrocera tryoni — poses a significant threat to horticultural production in Victoria causing losses of fruit and jeopardising access to interstate and international markets. The Victorian Government implements and largely funds an area freedom program to manage QFF. Concern about the record number of outbreaks in 2007-08 and the escalating costs of maintaining the current management regime, led the Victorian Department of Primary Industries to review the program to identify improved strategies for managing QFF. As part of this work, a benefit cost analysis (BCA) of alternative strategies has been conducted. While the BCA method is well established, in general few studies are publicly available for area freedom programs. In this paper a number of the practical issues encountered in analysing area freedom are detailed, such as estimating welfare effects, how to consider social and environmental costs and benefits and incorporating risk for managing pests. Implications for policy and the design of future programs are discussed. The approach and issues identified in this paper provide insights for other agencies undertaking similar BCAs to inform biosecurity policy.