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While the suprachiasmatic nucleus (SCN) coordinates many daily rhythms, some circadian patterns of expression are controlled by SCN-independent systems. These include responses to daily methamphetamine (MAP) injections. Scheduled daily injections of MAP resulted in anticipatory activity, with an increase in locomotor activity immediately prior to the time of injection. The MAP-induced anticipatory behavior is associated with the induction and a phase advance in the expression rhythm of the clock gene <i>Period1</i> (<i>Per1</i>). However, this unique formation mechanism of MAP-induced anticipatory behavior is not well understood. We recently developed a micro-photomultiplier tube (micro-PMT) system to detect a small amount of <i>Per1</i> expression. In the present study, we used this system to measure the formation kinetics of MAP-induced anticipatory activity in a single whisker hair to reveal the underlying mechanism. Our results suggest that whisker hairs respond to daily MAP administration, and that <i>Per1</i> expression is affected. We also found that elevated <i>Per1</i> expression in a single whisker hair is associated with the occurrence of anticipatory behavior rhythm. The present results suggest that elevated <i>Per1</i> expression in hairs might be a marker of anticipatory behavior formation.