To examine the neural correlates of contextually differing control mechanisms in saccade initiation, we studied 18 subjects who performed two saccade paradigms in a pseudo-random order, while their eye movements were recorded in the MRI scanner (1.5 T). In the gap task the fixation point was extinguished 200 ms before target onset, and in the overlap task the fixation point vanished 500 ms after target onset. Subjects were asked to maintain stable fixation in the fixation period and to quickly saccade to peripherally presented targets. Inter-individual activation differences were assessed using regression analyses at the second level, with mean saccadic reaction time (SRT) of subjects as a covariate. To identify brain regions varying with trial-by-trial changes in SRTs, we included SRTs as a parametric modulation regressor in the general linear model. All analyses were regions of interest based and were performed separately for the gap and overlap conditions. For the gap paradigm, we did not obtain activation in regions previously shown to be involved in preparatory processes with much longer gap periods. Interestingly, both inter- and intra-individual variability analyses revealed a positive correlation of activation in frontal and parietal eye-movement regions with SRTs, indicating that slower saccade performance is possibly associated with higher cortical control. For the overlap paradigm, the trial-by-trial variability analysis revealed a positive correlation of activation in the right opercular inferior frontal gyrus with SRTs, possibly linked to fixation-related processes that have to be overcome to perform a speeded saccade in presence of a fixation point.