Abstract Background The ability to perform objective pain assessment is very important in paediatric patients. The goal of this study was to investigate the relationship between the analgesia nociception index (ANI), which is based on the heart rate variability, and objective measurements of pain intensity in young or cognitively impaired children, after surgical or imaging procedures (control group) under general anaesthesia. Methods On arrival in the recovery room and subsequently at 5-10 min intervals, the level of pain was rated using the FLACC pain scale (0-10). The ANI values (0-100; 0 indicating the worst pain) were recorded simultaneously. The area under the receiver operating characteristic curve (AUC) and grey zone approach were used to evaluate the performance of the ANI to detect patients with FLACC >4. Instantaneous ANI values were compared with ANI values averaged over 256 s periods of time. Results All children in the surgical group (n=32) developed moderate-to-severe pain (FLACC >4). Children in the control group (n=30) exhibited minimal pain. Instantaneous ANI values were lower in children of the surgical group than in the control group 52 (sd16) vs 69 (16), P<0.001. The AUC for the 256 s ANI recording period 0.94 (95% confidence interval 0.85-0.99) was significantly higher than for instantaneous ANI (P<0.05). When measured for a period of 256 s, an ANI cut-off value of 56 (grey zone 58-60) was most predictive of a FLACC ≥4. Conclusions The ANI may provide an objective measurement of acute postoperative pain, which is correlated with that measured on a FLACC scale in young or cognitively impaired children.