Long duration usage of BCI systems may induce a loss of attention in the participant and result in a decrease of system performance. Therefore, investigation of fatigue during longtime usage and its effect on the signal quality are necessary for the use of BCI systems in daily life. In this study, 54 participants used BCI systems for about five hours, and it included the three major BCI paradigms. Participants conducted each paradigm once again at the end of the experiment. We investigated how fatigue changes as the experiment progresses and report the effect of fatigue on signal quality by comparing the first and second sessions. In the result, a significant increase was seen in questionnaire scores as well as in alpha-band power in the resting state. The signal quality decreased slightly in the MI and SSVEP paradigms, but the amplitude of the P300 in the ERP paradigm increased.