It is very important to determine the polycyclic aromatic hydrocarbon (PAH) emissions caused by the use of renewable fuels in diesel engines and to know the possible damages. This study investigates the emissions (regulated and unregulated) of biodiesel/n-pentanol mixtures, which are free of aromatic content, with emphasis on PAH formation and an examination of toxicity to public health and the environment. Engine failures caused by wetstacking are also discussed. Biodiesel/n-pentanol fuel mixtures with alcohol concentrations of 5%, 20%, and 35% by volume (v/v) served as test fuels in a compression ignition engine. A five-gas analyzer was used to measure hydrocarbon (HC), carbon monoxide (CO), and nitrogen oxide (NOx) emissions. Polycyclic aromatic hydrocarbons were detected and measured using gas chromatography-mass spectrometry (GC-MS). Against the baseline diesel fuel, the biodiesel/n-pentanol fuel blends and neat biodiesel reduced NOx emissions and produced significantly fewer PAHs and toxicity, confirming the significance of the aromatic content of the fuel. Biodiesel reduced total PAHs by 48.02% and the addition of 5% n-pentanol to biodiesel further decreased total PAHs by 21.26%. The total toxicity (BaPeq (benzo[a]pyrene equivalent)) as a result of biodiesel was 83.49% less than diesel. The addition of n-pentanol to biodiesel further reduced toxicity by 59.15%, 57.89%, and 48.33% for BPen5, BPen20, and BPen35 blends, respectively. In addition, n-pentanol was shown to be effective for reducing total PAH emissions, as well as heavier PAHs, which have greater carcinogenicity and pose a greater likelihood of engine damage from wetstacking when running in low-load conditions at cold temperatures.