Beneficial effects on obesity and dysmetabolism of a variety of functional ingredients contained in brown rice have attracted academic as well as clinical attention. On the other hand, it is noteworthy that the absorption efficiency of some of the functional ingredients derived from brown rice from the digestive tract is significantly low. Based on these backgrounds, we developed the “nanoparticulated brown rice germ extract” by encapsulating brown rice germ extract containing γ-oryzanol, one of the functional ingredients abundantly and specifically in brown rice (rice bran), in nanoparticles, and conducted safety and efficacy tests in humans. The present study was performed appropriately after the approval from the ethics committee of Hokkaido Information University. Japanese men and women whose BMI is 23 kg/m² or more and less than 25 kg/m², or 25 kg/m² or more and less than 30 kg/m², and whose visceral fat area is less than 100 cm² when measured by bioelectric-impedance methods were recruited for the study. We conducted a placebo-controlled, randomized, double-blind, parallel-group comparative study targeting approximately 78 people who met the eligible criteria, and examined metabolic improvements when the “nanoparticulated brown rice germ extract” tablets were ingested once-a-day continuously for 12 weeks. Although a decreasing trend was observed in the abdominal visceral fat area, which is a primary endpoint, there were no significant differences among the ingestion groups of test food (low dose group: 5 mg, and medium-dose group: 10 mg). Among the secondary endpoints, plasma LDL-cholesterol (LDL-C) level showed a marginally significant decrease in the medium and low dose (5 mg) groups compared to the control group (placebo ingestion) after 8 weeks of ingestion (p = 0.078, p = 0.098). The plasma lipid ratio (LDL-C/HDL-C) showed a significant decrease in the low dose group compared to the control group after 4 and 8 weeks of ingestion (p = 0.016, p = 0.018). The plasma non-HDL-C level showed a marginally significant or significant decrease in the medium and low dose groups compared to the control group after 8 weeks of ingestion (p = 0.099, p = 0.031). Blood level of HbA1c also showed a significant decrease in the medium-dose group compared to the control group after 4, 8, and 12 weeks of ingestion (p = 0.029, p = 0.011, p = 0.011). Furthermore, plasma level of adiponectin, which has potent anti-atherosclerotic actions, showed a marked increase in the high, medium, and low dose groups (p = 0.012, p = 0.039, p = 0.017) after 4 weeks of ingestion compared to the control group, and also showed a marginally significant or significant increase after 8 and 12 weeks of ingestion. During the hospital visit, problematic changes were not observed in blood pressure, pulse rate, general blood tests, liver and kidney functions, and urinalysis, and adverse events suggesting a causal relationship with the test food were not observed. This clinical intervention study confirmed the safety of ingestion of the “nanoparticulated brown rice germ extract”, which was also proven to improve the atherogenic lipid profile, reduce HbA1c level, and increase plasma adiponectin concentration. Results obtained tempt us to expect that nanoparticulated brown rice germ extract is well eligible for practical use.