Prolonged sitting (PS) in the workplace has been linked to a higher risk of developing non-communicable chronic diseases. Simultaneously, an elevated waist-to-height ratio (WHtR) is considered a reliable measure of increased risk for the same condition. The main objective of this research was to examine the relationship between workplace PS and increased WHtR among male workers from the Spanish region of Castilla y León. The secondary objective was to assess how age affects elevated WHtR in workers. This retrospective observational study was carried out in accordance with the STROBE guidelines. The sample included 85,670 male workers, categorized by job type (with or without PS) and age (<40 years or ≥40 years). Chi-square test (X²), Pearson correlation coefficients, and odd ratios (OR) were used to analyze associations. Among workers with PS, X² = 0.73 (p = 0.391) and 1.11 (p = 0.292) were reported, and among those without PS, X² = 0.86 (p = 0.354) and 1.24 (p = 0.265), for the years 2022 and 2023, respectively. Therefore, there was no significant association between workers with or without PS and an elevated WHtR, both in those younger than and older than 40 years of age. Advanced age (≥40 years) showed a significant association with increased WHtR (p < 0.01; OR = 2.6). However, no statistical association was observed between PS and elevated WHtR (p > 0.05; OR = 1.15). These findings suggest that age plays a more prominent role than occupational PS time in WHtR among male workers. Future studies should consider other factors, including physical activity and dietary habits, that could affect WHtR.