Occupation affects bone mineral density (BMD); however, only few studies have been published. This study evaluated the effect of working time during a day on BMD. The cross-sectional study involved 18- to 50-year-old people who reported their working time and were measured for BMD using dual-energy X-ray absorptiometry in the Fourth Korea National Health and Nutrition Examination Survey 2009. The time period of work was divided into "daytime" and "other than daytime." The other-than-daytime group included evening time, nighttime, regular shift time, and irregular shift time. Among 3,005 subjects, 2,378 were daytime workers and 627 were other-than-daytime workers. The mean BMD of the total femur and lumbar spine were significantly lower in other-than-daytime workers compared to daytime workers (femur 0.948 vs. 0.966 g/cm², respectively, p = 0.001; lumbar spine 0.976 vs. 0.988 g/cm², respectively, p = 0.023). The other-than-daytime group had lower levels of serum 25-hydroxyvitamin D than the daytime group (16.3 vs. 17.6 ng/mL, p < 0.001). The proportion of osteopenia (T score < -1.0) was higher in the other-than-daytime than the daytime group (34.3 vs. 29.1 %, p = 0.014). After adjustment for age, sex, socioeconomic status, lifestyle factors, daily intake of calcium, and vitamin D level, the relative risks of osteopenia of regular-shift and irregular-shift workers were significantly higher (1.65, 95 % CI 1.05-2.60; 1.78, 95 % CI 1.09-2.89) than those of daytime workers. These data suggest that other-than-daytime working, especially regular and irregular shift working, is associated with decreased BMD and increased risk for osteopenia in Korean adults.