A Boolean network is one of the models of biological networks such as gene regulatory networks, and has been extensively studied. In particular, a probabilistic Boolean network (PBN) is well known as an extension of Boolean networks, but in the existing methods to solve the optimal control problem of PBNs, it is necessary to compute the state transition diagram with 2(n) nodes for a given PBN with n states. To avoid this computation, an integer programming-based approach is proposed for a context-sensitive PBN (CS-PBN), which is a general form of PBNs. In the proposed method, a CS-PBN is transformed into a linear system with binary variables, and the optimal control problem is reduced to an integer linear programming problem. By a numerical example, the effectiveness of the proposed method is shown. Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved.