Identifying triggers for challenging behavior is difficult in some children with autism because of their limited communication abilities. Physiological indicators of stress may provide important insights. This study examined whether heart rate (HR) predicts challenging behavior in children with autism. While wearing an electrocardiograph monitor, 41 children with autism aged 2- to 4-years participated in tasks designed to induce low-level stress (e.g. waiting for a snack). Coders identified 106 time periods during which challenging behaviors occurred and also coded 106 randomly selected time samples that did not include challenging behaviors. Thirteen (32%) participants exhibited challenging behaviors and were included in the study. Baseline-corrected HR was computed for each behavior/time sample. On average, children with autism showed a 22 ± 16% HR increase from baseline 58 ± 22 seconds before the onset of a challenging behavior episode. Peak HR change had moderate predictive utility (area under the curve = .72, p < .001). The increase in HR before challenging behaviors was similar for children of different characteristics (age, autism severity, expressive language ability, overall developmental ability). Results highlight the promise of using physiological stress to predict challenging behavior in preschoolers with autism; although, they need to be replicated in larger samples. Given recent advances in wearable biosensing, it may be useful to incorporate HR monitoring in autism intervention. Lay summary In children with autism, changes in heart rate (HR) may help us predict when challenging behavior is about to occur - but this hypothesis has not been well studied. In this study, HR increase moderately predicted challenging behavior in preschoolers with autism. Given recent advances in wearable sensors, it may be useful to incorporate HR monitoring in autism intervention.