Blocking the abrupt increase in systolic blood pressure associated with autonomic response during bladder hydrodistention in patients with interstitial cystitis/bladder pain syndrome (IC/BPS) is essential for patient safety. We conducted this study to compare autonomic responses during bladder hydrodistention in patients with IC/BPS under general and spinal anaesthesia. Thirty-six patients were randomly allocated to a general anaesthesia (GA, n = 18) or a spinal anaesthesia (SA, n = 18) group. Blood pressure and heart rate were measured continuously and ΔSBP, defined as maximum increases in SBP during bladder hydrodistention from baseline, was compared between groups. Heart rate variability was analysed using electrocardiograms. The post-anaesthesia care unit assessed postoperative pain using a numeric (0–10) rating scale. Our analyses yield a significantly greater ΔSBP (73.0 [26.0–86.1]vs.2.0 [− 4.0 to 6.0] mmHg), a significantly lower root-mean-square of successive differences in heart rate variability after bladder hydrodistention (10.8 [7.7–19.8] vs. 20.6 [15.1–44.7] ms), and significantly higher postoperative pain scores (3.5 [0.0–5.5]vs.0.0 [0.0–0.0]) in the GA compared to the SA group. These findings suggest that SA has advantages over GA for bladder hydrodistention in preventing an abrupt increase in SBP and postoperative pain in IC/BPS patients.