BACKGROUND Binocular rivalry is a perceptual phenomenon that arises when two incompatible images are presented separately, one to each eye, and the observer experiences involuntary perceptual alternations between the two images. If the two images are flickering at two distinct frequencies, electroencephalography (EEG) can be used to track the frequency-tagged steady-state visually evoked potential (SSVEP) driven by each image as they compete for awareness, providing an objective measure of the subjective perceptual state. This spontaneous alternation in perceptual dominance is believed to be driven by neural processes across widespread regions in the brain, but the real-time mechanisms of these processes remain unclear. METHODS The goal of this study was to determine the feasibility of investigating binocular rivalry using a simultaneous EEG-fMRI approach in order to leverage the high temporal resolution of EEG with the high spatial resolution of fMRI. RESULTS We have developed novel techniques for artifact removal and signal optimization for the rivalry-related SSVEP data collected simultaneously during fMRI. METHODS Our methods address several significant technical challenges of recording SSVEP data in the noisy fMRI environment, and enabled us to successfully reconstruct SSVEP signatures of rivalry in a group of healthy human subjects. CONCLUSIONS Further development and application of these techniques will enable more comprehensive integration of EEG and fMRI data collected simultaneously and could have significant implications for EEG-fMRI studies of brain activity in general.