Objective <p>To investigate the effects of high-frequency repetitive transcranial magnetic stimulation (rTMS) over the left dorsolateral prefrontal cortex (DLPFC) in Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).</p> Methods <p>This was a randomized, double-blind, controlled study. We consecutively enrolled PD patients with MCI (PD-MCI) from the Second Affiliated Hospital of Soochow University from September 2021 to November 2022. The patients were randomly assigned to the active rTMS group (<i>n</i> = 15) and the sham rTMS group (<i>n</i> = 15), and received 10HZ rTMS over left DLPFC for 7 consecutive days. A battery of neuropsychological assessments was performed on participants pre-test and post-test, including attention, executive function, memory, language, and visuospatial function. A resting electroencephalograph (EEG) was recorded, and the absolute and relative power of delta, theta, low alpha, high alpha, and beta were compared between the two groups. Follow-up assessments were performed at baseline, 1 week, 4 weeks, and 3 months after rTMS treatment.</p> Results <p>Finally, 30 patients completed the follow-up. After 1 week of treatment, compared to baseline, the active group showed significant improvement on the Montreal Cognitive Assessment (MoCA) scale (<i>P</i> = 0.019), Auditory Verbal Fluency Test (AVLT) immediate recall (<i>P</i> = 0.001), AVLT long-delayed recall (<i>P</i> = 0.006), AVLT recognition (<i>P</i> = 0.015) and Boston naming (<i>P</i> = 0.012), while the time of Trail Making Test B (<i>P</i> = 0.022) was decreased. Compared to the sham group, a significant increase in the percentage change of the global relative high alpha power was shown in the active group (<i>P</i> = 0.012). The data showed an increase in the percentage change of the relative high alpha power in the left frontal region (<i>P</i> = 0.041). Moreover, the correlation analysis revealed that the MoCA score was positively correlated with the relative high alpha power (<i>P</i> = 0.004). There was no significant change in the sham group.</p> Conclusion <p>High-frequency rTMS over left DLPFC contributes to cognitive improvement in PD-MCI patients and increased relative high alpha power may be associated with cognitive improvement.</p> Trial registration <p>This study has been registered at Chinese Clinical Trial Registry (identifier: ChiCTR2000039557). Registered on 31 October 2020.</p>