The study of magnetodynamics using stroboscopic time-resolved x-ray photoemission electron microscopy (TR-XPEEM) involves an intrinsic timescale provided by the pulse structure of the synchrotron radiation. In the usual multi-bunch operation mode, the time span between two subsequent light pulses is too short to allow a relaxation of the system into the ground state before the next pump-probe cycle starts. Using a deflection gating mechanism described in this paper we are able to pick the photoemission signal resulting from selected light pulses. Thus, PEEM measurements can be carried out in a flexible timing scheme with longer delays between two light pulses. Using this technique, the magnetodynamics of both Permalloy and iron structures have been investigated. The differences in the dynamic response on a short magnetic field pulse are discussed with respect to the magnetocrystalline anisotropy.