The possibility that different neural systems are used to measure temporal durations at the sub-second and several second ranges has been supported by pharmacological manipulation, psychophysics, and neural network modelling. Here, we add to this literature by using fMRI to isolate differences between the brain networks which measure 0.6 and 3s in a temporal discrimination task with visual discrimination for control. We observe activity in bilateral insula and dorsolateral prefrontal cortex, and in right hemispheric pre-supplementary motor area, frontal pole, and inferior parietal cortex during measurement of both intervals, suggesting that these regions constitute a system used in temporal discrimination at both ranges. The frontal operculum, left cerebellar hemisphere and middle and superior temporal gyri, all show significantly greater activity during measurement of the shorter interval, supporting the hypotheses that the motor system is preferentially involved in the measurement of sub-second intervals, and that auditory imagery is preferentially used during measurement of the same. Only a few voxels, falling in the left posterior cingulate and inferior parietal lobe, are more active in the 3s condition. Overall, this study shows that although many brain regions are used for the measurement of both sub- and supra-second temporal durations, there are also differences in activation patterns, suggesting that distinct components are used for the two durations.