There is limited evidence examining the association between B vitamin supplementation and improved endothelial function via lowering plasma homocysteine levels. This study investigated whether low-dose B vitamin supplementation improves endothelial dysfunction in Japanese adults with one or more components of metabolic syndrome. A randomized, controlled, crossover trial, without a washout period or blinding of subjects, was conducted from May-September, 2010. The subjects were 127 Japanese men and women aged 40–65 years who had at least one component of metabolic syndrome without medication. Participants took a supplement drink for two months but were divided into early intervention or later intervention groups. The flow-mediated dilatation, plasma homocysteine level, serum B-vitamins, and vitamin C levels were measured. A significant increase in serum B vitamins and vitamin C levels, and a reduction in plasma homocysteine levels were observed. The mean serum homocysteine level pre- and post-intervention was 9.8 and 8.2 µmol/L in the early intervention group and 10.8 and 7.4 µmol/L in the later intervention group (p<0.01). However, no significant changes in flow-mediated dilatation was found. Low-dose multivitamin supplementation including B vitamins is associated with a significant reduction in plasma homocysteine levels among patients with one or more components of metabolic syndrome. This study was registered at the University Hospital Medical Information Network (UMIN) centre, and has the identifier UMIN000004436.