Many important problems in agricultural and natural resource economics concern an intertemporal choice between alternate dynamic systems. This significance has motivated a theoretical literature generalizing the necessary conditions of Optimal Control Theory to multiple-phase problems. However, gaining detailed insight into their practical management is difficult because general numerical solution methods are not available. This paper resolves this deficiency through the development of a flexible and efficient computational algorithm based on a set of necessary conditions derived for finite-time, multiple-phase systems. Its effectiveness is demonstrated in an application to a nontrivial crop rotation problem.