Given a graph $G$ and two independent sets $S, T$ of $G$, the independent set reconfiguration problem is the problem to determine whether $T$ can be obtained by repleatedly removing and adding a vertex from and to $S$, while intermediate sets must be also independent. This paper proposes an algorithm for the independent set reconfiguration problem using a data structure, called zero-suppressed binary decision diagrams (ZDDs). This algorithm can be generalized to various reconfiguration problems.