Women who undergo cesarean delivery have reported experiencing mood distress related to the surgery and postoperative pain. Heart rate variability biofeedback (HRVB) training is known to have positive effects on mental health, but its effects on women undergoing cesarean delivery have not yet been determined. This study evaluated the effects of an HRVB training intervention on stress, anxiety, and depression in women undergoing cesarean delivery. We hypothesized that 10 sessions of HRVB training could cumulatively improve emotion regulation in participants. This study was designed as a double-blinded randomized controlled trial involving a total of 86 enrolled women who were then divided into two groups: intervention and control. During their hospitalization, the intervention group underwent HRVB training daily, while both groups received standard perinatal care. Heart rate variability (HRV) was assessed using root mean square of successive differences (RMSSD), standard deviation of normal-to-normal intervals (SDNN), high-frequency power (HF) and low-frequency power (LF). HRV parameters, stress, anxiety, and depression were evaluated at baseline and on the fifth day after childbirth. Intention-to-treat (ITT) analyses examined change over time between groups. Although no significant effects were found for the RMSSD and HF, a significant increase was observed in SDNN (F = 13.43, p = < 0.001, ƞ2 = 0.14), and LF at post-assessment (F = 4.26, p = .04, ƞ2 = 0.05) compared to the control group. Except for the depression variable, stress (F = 6.11, p = .02, ƞ2 = 0.07) and anxiety (F = 8.78, p = .004, ƞ2 = 0.10) significantly decreased compared to the control group on the fifth postpartum day. Furthermore, post-hoc analysis showed that HRVB was more effective in decreasing mild to severe depressive symptoms (F = 7.60, p = .001, ƞ2 = 0.27). The intervention program successfully decreased self-perceived stress and anxiety in the postpartum period and relieved symptoms in more severely depressed participants. Our findings suggest that this program is suitable and beneficial for application in women during the early postpartum period following cesarean delivery.