Background Low Back Pain (LBP) is associated with an increase in disability-adjusted life years, and increased risk of disability retirement and greater absenteeism in Brazil. Hence, evidence on healthcare and lost productivity costs due to LBP is of utmost importance to inform decision-makers. Methods Cost-of-illness study with top-down approach, and societal perspective. We extracted data from National databases, considering the period 2012–2016. Outpatient expenses included clinical, surgical, diagnosis, orthosis/prosthetics, and complementary actions. Inpatient care expenses included hospital and professional services, intensive care unit, and companion stay. For productivity losses, duration of work absence and associated information (work-related and non-work-related; value of the sickness absence benefit; age; gender; and economic activity) were analyzed. Lost productivity costs were calculated multiplying the absence from work (days) by the daily-benefit. Results The societal costs amounted to US$ 2.2 billion, and productivity losses represented 79% of the costs. Total healthcare expenses were estimated to US$ 460 million. We found more than 880,000 diagnostic images. Individuals with LBP were in total 59 million days absent from work between 2012–2016. The mean lost days absent from work per person, for each year investigated was, respectively, 88; 84; 83; 87; and 100. Men were more days absent from work than women. In addition, rural workers presented greater absence from work compared to other professional activities. Conclusion Healthcare expenses and lost productivity costs due to LBP were substantial, hence, there is a need for improvement of health services and policies to deal with this increasing burden of illness. We found an extensive use of diagnostic imaging, which is rather discouraged by clinical guidelines. We assume that men were experiencing high levels of back pain disability compared with women, as they presented greater absenteeism and higher lost productivity costs.