The dataset comprises 73 archaeological and historical sites across Borneo, a valuable resource for researchers interested in regional Bornean human occupation and settlement. It covers a period of 45 ka before the present (BP) to 0 BP (1950 CE), with a specific focus on the last 6 ka BP. The dataset provides detailed information on the location, timing, and duration of human occupation at each site, based on archaeological surveys. This compilation enables the study of resource use and their landscape legacies, making it an indispensable tool for understanding the regional Bornean human occupation and settlement. The archaeological site database was constructed based on a review of published reports and articles (see Perez-Cardenas et al., 2024). We reviewed and categorized each record between i) no radiocarbon data, such as U-series and U-Th dating, ii) calibrated radiocarbon, and iii) uncalibrated radiocarbon. Then, calibrated and uncalibrated radiocarbon were recalibrated to 95.4% confidence using the atmospheric curve IntCal20, OxCal 4.4 (Reimer et al., 2020). The dates obtained using Uranium were not calibrated. The lab code used in the original reference is provided for each record. We subset the dataset, obtaining 47 archaeological sites, by selecting sites with records over the last 6 ka BP to extract environmental characteristics. We created a matrix with the time and duration of occupation of archaeological evidence in 100-year intervals from 6 ka BP to 0 BP (1950 CE) for each site.