While a number of models have been developed to assist managers of deciduous fruit tree crops with specific aspects of decision making, most are non-optimising predictive models and few employ detailed mechanistic models of fruit-tree growth that would enable the simulation of any orchard system from planting to maturity. This paper details the complex biological and economic relationships present in an apple orchard system and describes a dynamic simulation model based on these interactions. The model is bioeconomic in nature, and may be used to investigate a range of issues of relevance to the commercial apple orchardist. These issues include understanding how biological factors influence apple-tree productivity, and how to choose among a diverse range of apple orchard systems. Each system, consisting of a particular combination of cultivar, rootstock, tree spacing and training method, has implications for fruit quality, quantity and ultimately profit. The choice of system is made at planting, while an important annual decision is the optimal rate of thinning, both of which determine potential yield over the lifetime of the orchard. These decisions also influence costs and revenues per hectare and, by necessity, are made in the context of unknown future prices of inputs and outputs. The bioeconomic model is used to maximise net present value of one orchard system by selecting optimal thinning strategies over a 15-year period.