Auditory hyper‐reactivity is a common sensory–perceptual abnormality that interrupts behavioral adaptations in autism spectrum disorders (ASD). Recently, prolonged acoustic startle response (ASR) latency and hyper‐reactivity to weak acoustic stimuli were reported in children with ASD. Indexes of ASR and its modulation are known to be stable biological markers for translational research in the adult population. However, little is known about the stability of these indexes in children. Thus, the objective of our study was to investigate the stability of neurophysiological ASR indexes in children with ASD and typical development (TD). Participants included 12 children with ASD and 24 with TD. Mean startle magnitudes to acoustic stimuli presented at 65–105 dB in increments of 10 dB were analyzed. Average peak startle latency (PSL), ASR modulation of habituation, and prepulse inhibition were also analyzed. These startle measures were examined after a follow‐up period of 15.7 ± 5.1 months from baseline. At both baseline and in the follow‐up period, children with ASD had significantly greater startle magnitudes to weak stimuli of 65–85 dB and more prolonged PSL compared with controls. Intraclass correlation coefficients for these ASR measures between both periods were 0.499–0.705. None of the ASR measures differed significantly between the two periods. Our results suggest that prolonged PSL and greater startle magnitudes to weak stimuli in children with ASD might serve as moderately stable neurophysiological indexes of ASD. Autism Res 2016. © 2016 International Society for Autism Research, Wiley Periodicals, Inc. Autism Res 2017, 10: 673–679. © 2016 International Society for Autism Research, Wiley Periodicals, Inc.