Objectives This study aimed to explore the transfer rates of aflatoxins from several contaminated herbal medicines by fungi to their decoctions. Methods Five types of commonly used herbal medicines including Lilii Bulbus, Hordei Fructus Germinatus, Nelumbinis Semen, Polygalae Radix and Bombyx Batryticatus were selected as the examples. Raw herbal medicine samples were treated by ultrasonication-assisted extraction with 70% methanol and immunoaffinity column clean-up, and the decoctions were prepared following the commonly used boiling method with water for 2 h. Then, the optimized high-performance liquid chromatography with fluorescence detection (HPLC-FLD) method was validated for the quantitative analysis of four aflatoxins (AFG 2 , AFG 1 , AFB 2 and AFB 1 ) after postcolumn photochemical derivatization, which was proved to be reliable and sensitive. Key findings Aflatoxins were detected to be transferred from the herbal medicines to decoctions with significantly different transfer rates in the five types of herbal medicines. Quietly high transfer rates of 7.26-115.36% for AFG 2 , 4.37-26.37% for AFB 1 and 9.64-47.68% for AFB 2 were obtained. AFB 1 as the most toxic aflatoxin expressed the lowest transfer rate, but still exhibited high amount in the samples. Conclusions Therefore, the monitoring of aflatoxins in herbal medicines and their decoctions is in great urgency to ensure the security of consumers taking decoctions.