We consider synchronization by noise for stochastic partial differential equations which support traveling pulse solutions, such as the FitzHugh-Nagumo equation. We show that any two pulse-like solutions which start from different positions but are forced by the same realization of a multiplicative noise, converge to each other in probability on a time scale $σ^{-2} \ll t \ll \exp(σ^{-2})$, where $σ$ is the noise amplitude. The noise is assumed to be Gaussian, white in time, colored and periodic in space, and non-degenerate only in the lowest Fourier mode. The proof uses the method of phase reduction, which allows one to describe the dynamics of the stochastic pulse only in terms of its position. The position is shown to synchronize building upon existing results, and the validity of the phase reduction allows us to transfer the synchronization back to the full solution.