Background: Virtual reality and arm cycling have been reported as effective treatment to improve upper limb motor recovery in patients with stroke. Intermittent theta burst stimulation (iTBS) can increase ipsilesional cortical excitability, and has been increasingly used in patients with stroke. However, few studies examined the augmented effect of iTBS on neurorehabilitation program. In this study, we investigated the augmented effect of iTBS on virtual reality-based cycling training (VCT) for upper limb motor function in patients with stroke.Methods: In this randomized controlled trial, 23 patients with stroke were recruited. Each patient received either 15 sessions of iTBS or sham stimulation in addition to VCT on the same day. Outcome measures, including Modified Ashworth Scale Upper Extremity (MAS-UE), Fugl-Meyer Assessment Upper Extremity (FMA-UE) for body function, Action Research Arm Test (ARAT), Nine Hole Peg Test (NHPT), Box and Block Test (BBT) and Motor Activity Log (MAL) for activity and Stroke Impact Scale (SIS) for participation were assessed before and after the intervention. Paired t test was performed to evaluate the effectiveness after the intervention and analysis of covariance (ANCOVA) was conducted to compare the therapeutic effects between two groups.Results: At post-treatment, both groups showed significant improvement in FMA-UE and ARAT, while only the iTBS group demonstrated significant improvement in MAS-UE, BBT, NHPT, MAL and SIS. ANCOVA revealed that the iTBS group presented greater improvement than the sham group significantly in MAS-UE, NHPT and SIS, and with borderline significance in ARAT, BBT and MAL. There was no significant difference in FMA-UE between groups.Conclusions: Intermittent TBS showed augmented efficacy on VCT for reducing spasticity, improving gross motor function and manual dexterity, and increasing participation in daily life in stroke patients. This study provided an integrated innovative intervention, which may be a promising therapy to improve upper limb motor function recovery, especially manual dexterity, in stroke rehabilitation. However, this study has a small sample size, and thus a further larger-scale study is warranted to confirm the treatment efficacy.Trial registration: This trial was registered under ClinicalTrials.gov ID No. NCT03350087, retrospectively registered, on November 22, 2017.