The aim of this study was to compare the heart rate (HR) and the perceived exertion (PE) regulation of a training program in women and their effects on the cardiorespiratory responses. Twenty-seven women (mean age 22.4 ± 2.7 years) were randomly assigned to a control group (CG, n = 9), a heart rate group (HRG, n = 9), or a perceptive group (PG, n = 9). All subjects performed a maximal graded test (MGT) on a cycle ergometer before and after 6 weeks. The HR, V(O2)peak, maximal tolerated power (MTP), and PE were recorded during both MGTs. A 6-week interval training program was performed by both the HRG and PG. HR targets were used for the HRG and PE for the PG to readjust the power output. The results show that the V(O2)peak and the MTP increased significantly (p < 0.05) for both training groups, whereas the CG obtained no changes. As a consequence, PE could be a valuable tool to readjust the training load during an interval training program.