The effect of fatigue and drowsiness on brain-computer interface (BCI) performance was evaluated. 20 healthy participants performed a standardized 11-minute calibration of a Rapid Serial Visual Presentation BCI system five times over two hours. For each calibration, BCI performance was evaluated using area under the receiver operating characteristic curve (AUC). Self-rated measures were obtained following each calibration including the Karolinska Sleepiness Scale and a standardized boredom scale. Physiological measures were obtained during each calibration including P300 amplitude, theta power, alpha power, median power frequency and eye-blink rate. There was a significant decrease in AUC over the five sessions. This was paralleled by increases in self-rated sleepiness and boredom and decreases in P300 amplitude. Alpha power, median power frequency, and eye-blink rate also increased but more modestly. AUC changes were only partly explained by changes in P300 amplitude. There was a decrease in BCI performance over time that related to increases in sleepiness and boredom. This worsened performance was only partly explained by decreases in P300 amplitude. Thus, drowsiness and boredom have a negative impact on BCI performance. Increased BCI performance may be possible by developing physiological measures to provide feedback to the user or to adapt the classifier to state.