In this paper, we propose a polar coding based scheme for set reconciliation between two network nodes. The system is modeled as a well-known Slepian-Wolf setting induced by a fixed number of deletions. The set reconciliation process is divided into two phases: 1) a deletion polar code is employed to help one node to identify the possible deletion indices, which may be larger than the number of genuine deletions; 2) a lossless compression polar code is then designed to feedback those indices with minimum overhead. Our scheme can be viewed as a generalization of polar codes to some emerging network-based applications such as the package synchronization in blockchains. Some connections with the existing schemes based on the invertible Bloom lookup tables (IBLTs) and network coding are also observed and briefly discussed.