This manuscript presents two studies on the effect of mindfulness meditation on duration judgment and its relationship to the subjective experience of time when the interval durations are on the second or the minute time scale. After the first 15 minutes of a 30-min meditation or control exercise, meditation-trained participants judged interval durations of 15 to 50 s or 2 to 6 min, during which they performed either a mindfulness meditation exercise or a control exercise. The participants' scores on the self-reported scales indicated the effectiveness of the meditation exercise, as it increased the level of present-moment awareness and happiness and decreased that of anxiety. The results showed an underestimation of time for the short interval durations and an overestimation of time for the long intervals, although the participants always reported that time passed faster with meditation than with the control exercise. Further statistical analyses revealed that the focus on the present-moment significantly mediated the exercise effect on the time estimates for long durations. The inversion in time estimates between the two time scales is explained in terms of the different mechanisms underlying the judgment of short and long durations, i.e., the cognitive mechanisms of attention and memory, respectively.