Can the rapid stream of conscious experience be predicted from brain activity alone? Recently, spatial patterns of activity in visual cortex have been successfully used to predict feature-specific stimulus representations for both visible and invisible stimuli. However, because these studies examined only the prediction of static and unchanging perceptual states during extended periods of stimulation, it remains unclear whether activity in early visual cortex can also predict the rapidly and spontaneously changing stream of consciousness. Here, we used binocular rivalry to induce frequent spontaneous and stochastic changes in conscious experience without any corresponding changes in sensory stimulation, while measuring brain activity with fMRI. Using information that was present in the multivariate pattern of responses to stimulus features, we could accurately predict, and therefore track, participants' conscious experience from the fMRI signal alone while it underwent many spontaneous changes. Prediction in primary visual cortex primarily reflected eye-based signals, whereas prediction in higher areas reflected the color of the percept. Furthermore, accurate prediction during binocular rivalry could be established with signals recorded during stable monocular viewing, showing that prediction generalized across viewing conditions and did not require or rely on motor responses. It is therefore possible to predict the dynamically changing time course of subjective experience with only brain activity.