Background: Obesity and overweight are associated with work absenteeism of medical cause. However, there is little knowledge on the relationship between incremental body mass index (BMI) and absenteeism. Objective: To assess the effect of annual increase in BMI on amount of prolonged absenteeism. Methods: Data from a longitudinal historical cohort of workers of a mining camp in Peru between 2006 and 2014 were used for the analysis. Prolonged absenteeism of 30 days or more in one year was chosen as the dependent variable; annual increase in BMI was considered as the explanatory variable. Regression analysis with generalized estimating equation was used to determine the relative risk adjusted for age, sex and type of work. Results: There were 1347 cases of medical leave reported with a median of 6 days. Of all cases of medical leave, 11% of those who had an annual increase in BMI and 6% of those who maintained their BMI were cases of prolonged absenteeism. Prolonged absenteeism significantly increased in workers who had an annual increment in BMI (adj RR 1.16, 95% CI 1.05 to 1.29). Conclusion: The annual increase in BMI was marginally associated with prolonged absenteeism. Temporal increment in BMI, regardless of the baseline BMI, may be an independent determinant of the work absenteeism of medical cause.