While the session-RPE (rating of perceived exertion) method can quantify training volume in athletes, this method is not able to evaluate energy expenditure (EE) during a training session. We developed an RPE-based activity record for assessing EE during athletic training, and we compared its results to those obtained using the flex-heart rate (flex-HR) method. The EE of nine female collegiate endurance runners was assessed by the RPE-based activity record and flex-HR methods during eight days in the normal training season. Subjects were asked to record their RPE in the record at 5-minute intervals, and to wear a HR monitor during training. All subjects also participated in an incremental treadmill exercise test, which was used to determine their RPE-EE and HR-EE regression equations. Although the RPE-based activity record significantly overestimated EE (RPE-activity record, 572 kcal/session; flex-HR method, 499 kcal/session; p = 0.031), it had high validity relative to the flex-HR method (intra-class correlation coefficient, 0.891; 95% confidence interval, 0.845–0.923) and there were no systematic errors in EE estimation between the two methods. Therefore, the RPE-based activity record can be used to assess EE during training in female runners. However, RPE-based activity record might overestimate EE for athletes who have more intermittent activities during training than endurance runners, because RPE takes more time for returning to the resting level than HR when the intensity of activity declines. Further research is needed to verify the validity of the RPE-based activity record for assessing EE during other sporting activities or measurement conditions, and to identify the factors affecting the degree of estimation error associated with this method.