Objectives To observe the effects of infra-low frequency transcranial magnetic stimulation （ILF-TMS） in insomnia after ischemic stroke. Methods A total of 60 insomniacs after ischemic stroke were divided into the conventional treatment group（ n=30） and the ILF-TMS group（ n=30） by random number table method. Zolpidem tartrate was prescribed to patients in both groups， 5mg orally per night before sleep. On this basis， the ILF-TMS group was treated with ILF-TMS， while the conventional treatment group received sham ILF-TMS treatment. Pittsburgh Sleep Quality Index（ PSQI） and polysomnography（ PSG） were used to evaluate the sleep status before and 10 days after the treatment. PSG was taken to evaluate the sleep state mainly through the percentage of time of total sleep time（ TST）， sleep latency（ SL）， non-rapid eye movement（ NREM） and rapid eye movement（ S1， S2， S3+S4）. Results Before the treatment there were no significant differences in the average scores of PSQI， TST， SL， S1， S2， S3+S4， REM between the two groups. In the conventional treatment group， the PQSI score decreased significantly after 10 days' treatment（ 18.03±1.37） vs（ 12.60±2.43）； TST prolonged from（ 251.42±42.42） min to（ 288.80±40.32） min； SL shortened from（ 39.60±17.62） min to（ 34.40±14.89）， all the differences were statistically significant（ P ＜ 0.05）. However， REM of sleep structure， S1， S2 and S3+S4 showed no significant changes compared with that before treatment. The PQSI score in the ILF-TMS group was significantly changed after therapy（ 18.17±1.29） vs（ 10.40±2.13）. Both TST and SL were improved （241.50±51.75） vs（ 353.45±52.20） and（ 40.80±17.47） vs（ 26.60±13.22）， with statistically significant differences（ P ＜ 0.05）. However， REM of sleep structure， S1， S2 and S3+S4 showed no significant changes compared with that before treatment. After treatment， the subjective scores of PSQI in the ILF-TMS group was significantly lower than those in the conventional treatment group， TST was significantly better than that in the conventional treatment group， and SL was also improved comparing with the conventional treatment group（ P＜0.05）. Conclusions Although short-term（ 10 days） ILF-TMS treatment cannot improve the sleep structure of patients with insomnia after ischemic stroke，ILF-TMS can improve the symptoms of insomnia after ischemic stroke.