Introduction: Although repetitive transcranial magnetic stimulation (rTMS) is efficacious for motor neuromodulation in stroke survivors, high interindividual variability for responsiveness remains a concern. Target probing on the skull using a proper brain-mapping technique may help overcome this challenge. This study assessed the feasibility of functional near-infrared spectroscopy (fNIRS) as a target navigator in rTMS treatment for motor facilitation in patients with stroke. Methods: Fifty-one patients with stroke were enrolled in this randomized controlled study. The patients were assigned to three groups: fNIRS-guided rTMS treatment (fNIRS group, n = 20), motor evoked potential (MEP)-guided rTMS treatment (MEP group, n = 16), and sham (n = 15) group. Motor assessments, including Fugl–Meyer Assessment (FMA), Wolf Motor Function Test (WMFT), and muscle strength, were conducted at baseline and after the 10-session rTMS treatment. Results: The fNIRS-guided hotspot (fNIRS-HS) was obtained for each patient, even those for whom the MEP-guided hotspot was undetectable. Both intervention groups exhibited significant improvements in muscle strength, FMA, and WMFT scores (P < 0.001) compared with the sham group. The fNIRS group achieved significantly greater improvement in elbow function (P = 0.001) than the MEP group. Conclusion: fNIRS can be a reliable tool for hotspot navigation for motor neuromodulation in patients with stroke. With high sensitivity to cortical oxygenation changes, this navigation system achieved a superior outcome to the traditional MEP-based method in patients with stroke. fNIRS-based systems may also facilitate the integration of machine learning, thus enabling precision medicine for neuromodulation. Trial Registration: https://clinicaltrials.gov; Unique identifier: NCT02006615.