To solve the problem of the deterioration in precision time protocol (PTP) synchronization performance caused by uncertainty queue waiting in packet transmission, this paper proposed a packet delay estimation algorithm with minimum queue waiting. Since the packet delay could be estimated with the lucky packets selected from stacks, the PTP synchronization performance would be improved. The boundary conditions of the proposed algorithm was decided by the mean time interval using the selection of “lucky packets” and its expression was deduced. Some meaningful tests indicate that in the asymmetry network, the accuracy of packet delay estimation increases almost 25ns with stability increasing almost 2 orders, and the accuracy of PTP synchronization increases more than onefold with stability increasing almost fourfolds, compared with no optimization.