Heart rate variability (HRV) is closely related to changes in the autonomic nervous system (ANS) associated with stress and pain. In this study, we investigated whether HRV could be used to assess cancer pain in mice with peritoneal metastases. At 12 days after cancer induction, positive indicators of pain such as physiological characteristics, appearance, posture, and activity were observed, and time- and frequency-domain HRV parameters such as mean R-R interval, square root of the mean squared differences of successive R-R intervals, and percentage of successive R-R interval differences greater than 5 ms, low frequency (LF), high frequency (HF), and ratio of LF and HF power, were found to be significantly decreased. These parameters returned to normal after analgesic administration. Our results indicate that overall ANS activity was decreased by cancer pain and that HRV could be a useful tool for assessing pain.