Motor imagery-based brain-computer interfaces (BCIs) have been studied without controlling subjects' gaze fixation position previously. The effect of gaze fixation and covert attention on the behavioral performance of BCI is still unknown. This study designed a gaze fixation controlled experiment. Subjects were required to conduct a secondary task of gaze fixation when performing the primary task of motor imagination. Subjects' performance was analyzed according to the relationship between motor imagery target and the gaze fixation position, resulting in three BCI control conditions, i.e., congruent, incongruent, and center cross trials. A group of fourteen subjects was recruited. The average group performances of three different conditions did not show statistically significant differences in terms of BCI control accuracy, feedback duration, and trajectory length. Further analysis of gaze shift response time revealed a significantly shorter response time for congruent trials compared to incongruent trials. Meanwhile, the parietal occipital cortex also showed active neural activities for congruent and incongruent trials, and this was revealed by a contrast analysis of R-square values and lateralization index. However, the lateralization index computed from the parietal and occipital areas was not correlated with the BCI behavioral performance. Subjects' BCI behavioral performance was not affected by the position of gaze fixation and covert attention. This indicated that motor imagery-based BCI could be used freely in robotic arm control without sacrificing performance.