In Japan, standing while working has not yet become commonplace, and there is little evidence to support the benefits of standing during the workday. Therefore, this study assessed the relationship between the introduction of a sit–stand desk and its ability to reduce the negative effects of sitting too long and increase employees’ general health and productivity. Seventy-four Japanese desk workers participated in this three-month intervention study. Using a randomized controlled trial, the participants were divided into intervention (n = 36) and control (n = 38) groups. The participant characteristics were ascertained using a questionnaire. The intervention effectiveness was assessed by measuring health-, physical activity-, and work-related outcomes. The results indicate that the intervention group significantly decreased their sitting time at work (p = 0.002) and had reduced neck and shoulder pain (p = 0.001). There was a significant increase in subjective health (p = 0.002), vitality in work-related engagement (p < 0.001), and self-rated work performance over a four-week period (p = 0.017). These findings indicate a significant difference between the two groups, demonstrating the effectiveness of a sit–stand desk in reducing sedentary behavior and improving workers’ health and productivity. Future research can accumulate further evidence of best practice use of sit–stand desks.