Background Cerebral autoregulation plays an important role in safeguarding adequate cerebral perfusion and reducing the risk of secondary brain injury, which is highly important for patients in the neurological intensive care unit (neuro-ICU). Although the consensus white paper suggests that a minimum of 5 min of data are needed for assessing dynamic cerebral autoregulation with transfer function analysis (TFA), it remains unknown if the length of these data is valid for patients in the neuro-ICU, of whom are notably different than the general populations. We aimed to investigate the effect of data length using transcranial Doppler ultrasound combined with invasive blood pressure measurement for the assessment of dynamic cerebral autoregulation in patients in the neuro-ICU. Methods Twenty patients with various clinical conditions (severe acute encephalitis, ischemic stroke, subarachnoid hemorrhage, brain injury, cerebrovascular intervention operation, cerebral hemorrhage, intracranial space-occupying lesion, and toxic encephalopathy) were recruited for this study. Continuous invasive blood pressure, with a pressure catheter placed at the radial artery, and bilateral continuous cerebral blood flow velocity with transcranial Doppler ultrasound were simultaneously recorded for a length of 10 min for each patient. TFA was applied to derive phase shift, gain, and coherence function at all frequency bands from the first 2, 3, 4, 5, 6, 7, 8, 9, and 10 min of the 10-min recordings in each patient on both hemispheres. The variability in the autoregulatory parameters in each hemisphere was investigated by repeated measures analysis of variance. Results Forty-one recordings (82 hemispheres) were included in the study. According to the critical values of coherence provided by the Cerebral Autoregulation Research Network white paper, acceptable rates for the data were 100% with a length >= 7 min. The final analysis included 68 hemispheres. The effects of data length on trends in phase shift in the very low frequency (VLF) band (F-1.801,F-120.669 = 6.321, P = 0.003), in the LF band (F-1.274,F-85.343 = 4.290, P = 0.032), and in the HF band (F-1.391,F-93.189 = 3.868, P = 0.039) were significant for 3-7 min, for 4-7 min, and for 5-8 min, respectively. Effects were also significant on the gain in the VLF band (F-1.927,F-129.134 = 3.215, P = 0.045) for 2-8 min and on the coherence function in all frequency bands (VLF F-2.846,F-190.671 = 90.247, P < 0.001, LF F-2.515,F-168.492 = 55.770, P < 0.001, HF F-2.411,F- 161.542 = 33.833, P < 0.001) for 2-10 min. Conclusions Considering the acceptable rates for the data and the variation in the TFA variables (phase shift and gain), we recommend recording data for a minimum length of 7 min for TFA in patients in the neuro-ICU.