Objective To investigate the effects of ultralow-frequency transcranial magnetic stimulation （TMS） on sleep deprivation-induced anxiety and cognitive capability deficit in rats. Methods A total of 18 SD rats were randomly divided into three groups： control group， sham group and TMS group. The sleep deprivation model was established by using improved multi-platform sleep deprivation method and the head of rat was stimulated by a homemade portable TMS instrument. TMS was performed once a day with 15 consecutive single stimulation（ interval between two single stimulation was 30 s） for 6 consecutive days. Body weight was monitored during the experiment. Behavioral analysis such as open field test， elevated plus maze and Morris water maze were adopted to evaluate the anxiety and cognitive capability in rats. Results Compared with con group， the body weight of sham group significantly decreased after 5 days' sleep deprivation. The results of open field test and elevated plus maze test showed that compared with con group， the percentage time in central area， percentage time in open arms， and percentage entries into open arms significantly decreased in sham group after 5 days' sleep deprivation. Morris water maze test showed that compared with con group， the latency to platform significantly increased， meanwhile， the duration in target quadrant significantly decreased in sham group after 6 days' sleep deprivation. There was no significant difference in above all indexes was found between TMS group and sham group. Conclusions Under this experimental condition， the ultralow-frequency TMS intervention cannot improve sleep deprivation induced anxiety and cognitive capability deficit in rats.