The blood lead reference value (BLRV) is used for guiding lead prevention and control measures. It is usually defined as the 97.5th percentile of the population-based blood lead level in each country. This study aims to determine the BLRV and factors associated with elevated (≥5 µg/dL) blood lead levels among children aged 1–5 years in Thailand. A cross-sectional study was conducted using secondary data extracted from a national survey, implemented in 171 hospitals during October 2018–September 2019. Demographic characteristics and potential risk factors including lead-related industries were collected. Multilevel logistic regression was used. Of 3,184 children included in the survey, the BLRV was 6.9 µg/dL. Three significant risk factors were identified: living near a lead factory (adjusted odds ratio (AOR) 2.09, 95% CI 1.27–3.42), exposure to the manufacture of fishing tackle (AOR 4.39, 95% CI 1.54–12.50), and exposure to the manufacture of shot and ammunition (AOR 6.30, 95% CI 1.81–21.93). Despite a calculated BLRV of 6.9 µg/dL, we propose a BLRV of 5 μg/dL in Thailand based on guidelines from the United Kingdom. Surveillance of blood lead levels should be established among children at high risk of lead exposure.