ObjectiveThis study aimed to explore the therapeutic effect of high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) with two different inter-train intervals (ITIs) on upper limb motor function in the early period of stroke.MethodsWe recruited 48 post-stroke patients in the early period and randomly divided them into three cohorts: the sham group, the short ITI (8 s) group, and the long ITI (28 s) group. HF-rTMS was delivered at 20 Hz. The amplitude of motor evoked potentials at the affected cortical region, representing the abductor pollicis brevis muscle, reflected cortical excitability. At baseline, immediately after treatment, and 1 month after treatment, we evaluated the recovery of upper limb motor function using Brunnstrom recovery stages (BRSs) and the Fugl–Meyer Assessment for upper extremity (FMA-UE), and assessed functional independence using the Barthel Index (BI).ResultsHF-rTMS with two different ITIs significantly improved upper limb functional recovery relative to the sham group, but there was no significant difference in cortical excitability changes or BRS, FMA-UE, or BI scores between the different ITI groups.ConclusionsAt the early post-stroke stage, HF-rTMS with short ITIs generates a similar therapeutic effect to HF-rTMS with long ITIs, suggesting that treatment times can be decreased.