ABSTRACT We present two different search methods for electromagnetic counterparts to gravitational-wave (GW) events from ground-based detectors using archival NASA high-energy data from the Fermi Gamma-ray Burst Monitor (GBM) and RXTE All-sky Monitor (ASM) instruments. To demonstrate the methods, we use a limited number of representative GW background noise events produced by a search for binary neutron star coalescence over the last two months of the LIGO-Virgo S6/VSR3 joint science run. Time and sky location provided by the GW data trigger a targeted search in the high-energy photon data. We use two custom pipelines: one to search for prompt gamma-ray counterparts in GBM, and the other to search for a variety of X-ray afterglow model signals in ASM. We measure the efficiency of the joint pipelines to weak gamma-ray burst counterparts, and a family of model X-ray afterglows. By requiring a detectable signal in either electromagnetic instrument coincident with a GW event, we are able to reject a large majority of GW candidates. This reduces the signal-to-noise ratio of the loudest surviving GW background event by around 15-20%.