Low vitamin D levels are associated with poorer outcomes after stroke. However, it is not clear whether post-stroke vitamin D supplementation can improve these outcomes. In this study, we investigated the effects of vitamin D supplementation on outcomes in hospitalized patients undergoing rehabilitation after acute stroke. A multicenter, randomized, controlled, double-blind, parallel-group trial was conducted from January 2012 through July 2017. One hundred patients admitted to a convalescent rehabilitation ward after having an acute stroke were randomized, and each one received either vitamin D3 (2000 IU/day) or a placebo. The primary outcome was a gain in the Barthel Index scores at week 8. Secondary outcomes were seen in Barthel Index efficiency, hand grip strength, and calf circumference at week 8. Ninety-seven patients completed the study. There were no significant differences in the demographic characteristics between the groups. The mean (±standard deviation) gain in the Barthel Index score was 19.0 ± 14.8 in the supplementation group and 19.5 ± 13.1 in the placebo group (p = 0.88). The Barthel Index efficiency was 0.32 ± 0.31 in the supplementation group and 0.28 ± 0.21 in the placebo group (p = 0.38). There were no between-group differences in the other secondary outcomes. Our findings suggest that oral vitamin D3 supplementation does not improve rehabilitation outcomes after acute stroke.