Elevated fasting plasma homocysteine (Hcy) level is a vascular disease risk factor. Plasma Hcy is affected by 5,10-methylenetetrahydofolate reductase (MTHFR) genotype and dietary folate intake. This cross-sectional study in 434 Japanese adults examined the associations among objectively measured physical activity (PA), plasma Hcy adjusting for dietary folate intake, and MTHFR C677T genotype. Daily PA was measured by triaxial accelerometry and all subjects completed a questionnaire about their dietary habits. Plasma Hcy and MTHFR C677T genotype were determined. Plasma Hcy in subjects with the TT genotype was significantly higher than in those with CC or CT genotype (p < 0.001). Plasma Hcy was significantly different between ≥ 200 (7.6 ± 0.2 nmol/mL) and <200 µg/day (8.3 ± 0.3 nmol/mL) folate intake groups (p = 0.003). There were no differences in plasma Hcy adjusting for age, sex, and folate intake between groups according to PA category in all subjects. However, there were significant interactions between time spent in light PA (p = 0.003), vigorous PA (p = 0.001), or inactivity (p = 0.004), and MTHFR genotype. In only the TT genotype, shorter time spent in light PA was associated with higher plasma Hcy than a longer time spent in light PA (11.5 ± 3.3 nmol/mL vs. 8.5 ± 3.3 nmol/mL, p < 0.001), and longer time spent in vigorous PA and inactivity were associated with higher plasma Hcy (11.8 ± 3.3 nmol/mL vs. 8.4 ± 3.2 nmol/mL, 11.6 ± 3.3 nmol/mL vs. 8.4 ± 3.3 nmol/mL, respectively, p < 0.001). In conclusion, light and vigorous PA were associated with plasma Hcy only in the TT genotype, but there were no such associations in all genotypes.