Sufficient knowledge on the work productivity impact of the health of fly-in fly-out (FIFO) workers in the mining sector in Australia is lacking. This study examined the impact of health and lifestyle behaviours on the work productivity of FIFO workers in the mining industry in Australia. FIFO workers completed an online questionnaire on health and work productivity loss measures. Linear regressions were used to model annual work productivity losses through absenteeism, presenteeism and total productivity loss. Workers with a high risk for health conditions were, on average, associated with 3.87% more productivity loss (absenteeism: 1.27% and presenteeism: 2.88%) than those with low risk. Workers who had multiple health risks classified as medium (3–4 health conditions) and high (5 or more health conditions) reported 1.75% and 7.46% more total productivity loss, respectively, than those with fewer multiple health risks (0–2 health conditions). Health conditions were estimated to account for an annual additional productivity cost due to absenteeism of AUD 8.82 million, presenteeism of AUD 14.08 million and a total productivity loss of AUD 20.96 million per 1000 workers. FIFO workers with high health risks experience more absenteeism, presenteeism and overall productivity loss. These measures provide strong economic justifications that could support the need for targeted workplace health interventions.