Green tea contains catechins, possessing anti-obesity and anti-oxidative effects, and has been consumed for hundreds of years. Our previous pilot study reported that Kosen-cha improves obesity and the parameters of metabolic syndromes in obese patients, however, the effect of Kosen-cha on obesity is still unclear in pre-obese subjects. The aim of this study was to investigate the effect of Kosen-cha on obesity and related clinical parameters including blood lipid and liver functions in a randomized placebo-controlled, double-blinded study. In total, 54 subjects with body mass index (BMI) of 25–30 were enrolled and randomized to receive either Kosen-cha or a placebo. The subjects drank Kosen-cha or the placebo thrice-daily for 12 weeks. Thereafter, we examined the effect of Kosen-cha on obesity (body weight, BMI, body fat, waist circumference, and visceral fat), lipid metabolism (triglyceride and high- and low-density lipoprotein cholesterol), and serum liver enzymes (aspartate aminotransferase, alanine aminotransferase (ALT), and γ-glutamyl transpeptidase). None of the subjects reported adverse effects from drinking Kosen-cha. Body weight, BMI, body fat, waist circumference, and visceral fat area remained unchanged in both groups. However, the change ratio of ALT significantly reduced between placebo and Kosen-cha groups after 12 weeks (Kosen-cha: −11.1 ± 32.7% vs. placebo: 8.46 ± 23.4%, p = 0.019). These results show that the consumption of Kosen-cha did not significantly improve obesity and may reduce liver enzyme levels in pre-obese Japanese subjects.