Mycotoxins are toxic fungal metabolites that may occur in crops. Mycotoxins may carry-over into bovine milk if bovines ingest mycotoxin-contaminated feed. Due to climate change, there may be a potential increase in the prevalence and concentration of mycotoxins in crops. However, the toxicity to humans and the carry-over rate of mycotoxins from feed to milk from bovines varies considerably. This research aimed to rank emerging and existing mycotoxins under different climate change scenarios based on their occurrence in milk and their toxicity to humans. The quantitative risk ranking took a probabilistic approach, using Monte-Carlo simulation to take account of input uncertainties and variabilities. Mycotoxins were ranked based on their hazard quotient, calculated using estimated daily intake and tolerable daily intake values. Four climate change scenarios were assessed, including an Irish baseline model in addition to best-case, worst-case, and most likely scenarios, corresponding to equivalent Intergovernmental Panel on Climate Change (IPCC) scenarios. This research prioritised aflatoxin B1, zearalenone, and T-2 and HT-2 toxin as potential human health hazards for adults and children compared to other mycotoxins under all scenarios. Relatively lower risks were found to be associated with mycophenolic acid, enniatins, and deoxynivalenol. Overall, the carry-over rate of mycotoxins, the milk consumption, and the concentration of mycotoxins in silage, maize, and wheat were found to be the most sensitive parameters (positively correlated) of this probabilistic model. Though climate change may impact mycotoxin prevalence and concentration in crops, the carry-over rate notably affects the final concentration of mycotoxin in milk to a greater extent. The results obtained in this study facilitate the identification of risk reduction measures to limit mycotoxin contamination of dairy products, considering potential climate change influences.