Background and objectives: The effects on anthropometry of several lipid-related foods for specified health uses (FOSHU) approved in Japan are not well known. We examined the effects of regular exercise and lipid-related FOSHU beverages on changes in body weight (BW) and waist circumference (WC) among factory and office workers. Materials and Methods: A total of 3002 subjects aged 20 years or older (2497 men and 505 women) received health check-ups in 2015 and 2016 and completed a lifestyle questionnaire. The association between regular exercise or lipid-related FOSHU beverage intake and changes in BW or WC were evaluated using trend test and linear regression analysis. Results: Regular exercise (≥1/week) was reported by 774 subjects (25.8%), and regular consumption of lipid-related FOSHU beverages (≥1/week) was reported by 1168 subjects (38.9%). The significant association between lipid-related FOSHU beverage intake and changes in BW was only observed among subjects with regular exercise (p for trend = 0.042). In the multivariable analysis, sex, older age, baseline weight, baseline body mass index (BMI), and regular exercise behavior were significantly associated with smaller changes in BW (p < 0.05). In WC, only the baseline values of WC and BMI were associated with one-year changes of WC. Conclusions: The combination of regular exercise and lipid-related FOSHU may be effective in maintaining BW.