While sensory processing latency, inferred from the manual reaction time (RT), is substantially affected by diverse stimulus parameters, subjective temporal judgments are relatively accurate. The neural mechanisms underlying this timing perception remain obscure. Here, we measured human neural activity by magnetoencephalography while participants performed a simultaneity judgment task between the onset of random-dot coherent motion and a beep. In a separate session, participants performed an RT task for the same stimuli. We analyzed the relationship between neural activity evoked by motion onset and point of subjective simultaneity (PSS) or RT. The effect of motion coherence was smaller for PSS than RT, but changes in RT and PSS could both be predicted by the time at which an integrated sensory response crossed a threshold. The task differences could be ascribed to the lower threshold for PSS than for RT. In agreement with the psychophysical threshold difference, the participants reported longer delays in their motor response from the subjective motion onset for weaker stimuli. However, they could not judge the timing of stimuli weaker than the detection threshold. A possible interpretation of the present findings is that the brain assigns the time marker for timing perception prior to stimulus detection, but the time marker is available only after stimulus detection.