Background: Cases for chronic kidney disease of unknown etiology (CKDu) are increasing in specific disease hotspots located in rural agricultural communities over Central America. The goal of the study was to estimate the prevalence and geographic distribution of self-reported work-related CKD and associated risk factors for CKDu by industry sector in Central America. Methods: We calculated the prevalence and distribution of self-reported CKD, work-related CKD, and suspected CKDu risk factors among the 9032 workers in the Second Central American Survey of Working Conditions and Health (II ECCTS, 2018). We mapped the distribution of suspected CKDu risk factors to work-related CKDu and weather conditions using average annual temperatures. Results: The primary and secondary industry sectors showed the highest proportion of males, suspected CKDu risk factors, and work-related CKD. Age (30–49 years: OR = 2.38, 95% CI 1.03–5.51), ethnicity (mestizo: OR, 7.44, 95% CI: 2.14–25.82), and exposure to high physical work demands (OR = 2.45, 95% CI: 1.18–5.09) were associated with work-related CKD. The majority of work-related CKD were reported in the western parts of Honduras and Nicaragua, in hot temperature regions, and overlapped with those areas with a high density of CKDu risk factors. Finally, some areas clustered CKDu risk factors without any work-related CKD points, mainly in the western part of Guatemala. Conclusion: Our findings supplement prior CKDu findings regarding a high prevalence of work-related CKD among 30- to 49-year-old mestizo males in the primary and secondary sectors, in hot temperature areas, in the central and western region, and overlapping with persons reporting two or more CKDu risk factors. Moreover, several geographic areas with CKDu risk factor clusters had no reported work-related CKD. These areas represent new industries and sectors to be monitored for possible future increases of CKDu cases.