Recent randomized clinical trials of a single infusion of mesenchymal stem cells (MSCs) for acute cerebral stroke revealed a limited functional recovery outcome. Conversely, animal studies suggest that multiple MSC infusions may enhance functional recovery by inducing neural plasticity, which indicates that a multiple-infusion approach might be effective for stroke treatment in humans. The objective of this study was to investigate whether multiple infusions of MSCs enhance functional outcomes during the acute phase of cerebral ischemia. Rats subjected to permanent middle cerebral artery occlusion (MCAO) were randomized into four groups: 1) vehicle group (infusion of vehicle only), 2) MSC-1 group (single administration of the standard MSC dose on day 3), 3) high-dose MSC group (single administration of three times the standard MSC dose on day 3), and 4) MSC-3 group (multiple administrations of the standard MSC dose on days 3, 10, and 17). MSCs were administered via the femoral vein. Behavioral performance and ischemic lesion volume were examined using in vivo MRI every 7 days from day 3 to day 45 after MCAO induction. The thickness of the corpus callosum (CC) was determined using Nissl staining, and the area of the CC was measured using ex vivo MRI. Interhemispheric connections within the CC were assessed using ex vivo MRI diffusion tensor imaging. The MSC-3 group exhibited the most significant motor recovery and increased CC thickness and area among all groups. Increased CC thickness and area were correlated with improved behavioral function 45 days after MCAO induction. Neural tracts through interhemispheric connections via the CC were most pronounced in the MSC-3 group, and this anatomical change showed a positive relationship with behavioral function. Multiple infusions of MSCs led to histological changes in the CC and neural tracts within the CC. These results indicate that multiple systemic infusions of MSCs had a greater beneficial effect in the acute phase of MCAO than a single standard or high-dose infusion of MSCs.