Objective To explore the effect of chloral hydrate on sleep Electroencephalogram (EEG) in children. Methods A total of 250 children under the age of 5 underwent EEG examination in West China Second University Hospital from Nov.8, 2019 to Sep.1,2021 were enrolled and divided into medication group or non-medication group according to whether they took chloral hydrate before the examination. Among them, 167 patients, the average age of whom was (30.78±17.43) months, were in the medication group, with a male to female ratio of 113:54. 83 cases were in the unmedicated group, the ratio of male to female was 60:23, and the average age was (33.12±17.10) months. There were no statistical difference in age and gender between the two groups. Quantitative EEG method was used to compare and analyze the percentages of the power of various EEG waveforms in the two groups. Results The proportion of EEG beta waves in the medication group was (2.76±4.03)%, and the proportion of EEG beta waves in the non-medication group was (1.59±1.21)%. There was a significant difference between the two groups. The proportion of sleep EEG beta waves in the medication group is higher. Conclusions Chloral hydrate may cause the increase of β fast waves in sleep EEG, which may affect the interpretation of EEG and the diagnosis of diseases.