Background Excess weight can increase absenteeism of workers and can have a negative influence on their productivity. Current evidence on this association is mostly based on cross-sectional data and there is little evidence concerning the longitudinal relationship between obesity, and disability with workplace absenteeism. Further, gender differences in this association have often ignored in the existing literature. Objectives This study aims to examine gender differences in the longitudinal association between obesity, and disability with absenteeism in the workplace. Methods Data from thirteen waves (2006 to 2018) of the Household, Income and Labour Dynamics in Australia (HILDA) survey were pooled, resulting in 117,769 observations for 19,851 adult employees. The Zero-Inflated Negative Binomial (ZINB) regression model was deployed to investigate the links between obesity, and disability with workplace absenteeism for the total sample and stratified by gender. Results The findings showed that overweight (Incidence Rate Ratio [IRR]: 1.23, 95% confidence interval [CI]: 1.02-1.47), obesity (IRR: 1.35, 95% CI: 1.12-1.64) and disability (IRR: 2.83, 95% CI: 2.36-3.38) were associated with prolonged workplace absenteeism irrespective of gender. This study found that the multiplicative interaction between weight status and gender is significantly associated with absenteeism. The results reveal that the rate of absenteeism was 2.79 times (IRR: 2.79, 95% CI: 1.96-3.97) and 1.73 times (IRR: 1.73, 95% CI: 1.20-2.48) higher among overweight and obese women than male counterparts, respectively. Moreover, this study found that the weight status of male workers is not associated with absenteeism. However, disability (IRR: 3.14, 95% CI: 2.43-4.05) is positively associated with longer days of absence among male workers. Finally, the study results showed that the rate of absenteeism is 1.82 (IRR: 1.82, 95% CI: 1.36-2.44), 1.61 (IRR: 1.61, 95% CI: 1.21-2.13), and 2.63 (IRR: 2.63, 95% CI: 1.99-3.48) times higher among overweight, obese, and female workers with a disability, respectively, compared with their lower weight counterparts. Conclusions Workplace absenteeism is significantly associated with overweight and obesity among Australian workers. An active workplace health promotion program is very important for weight management of overweight and obese workers and thus to reduce workplace absenteeism. For example, employers may provide incentives for maintaining recommended body weights, encourage exercise, and promote healthy diets amongst their workers.