Polycyclic aromatic hydrocarbons (PAHs) exhibit persistence in soils, and most of them are potentially mutagenic/carcinogenic and teratogenic for human beings but also influence the growth and development of soil organisms. The PAHs emitted into the atmosphere are ultimately deposited (by dry or wet deposition processes) onto the soil surface where they tend to accumulate. Soil organic matter (SOM) plays an important role in the fate and transformation processes of PAHs, affecting their mobility, availability, and persistence. Therefore, the aim of this research was to investigate the influence of SOM fractional diversification (fulvic acids—FA, humic acids—HA, and humins—HN) on PAH availability and persistence in soils. Twenty soil samples (n = 20) were collected from upper horizons (0–30 cm) of agricultural soils exposed to anthropogenic emissions from industrial and domestic sources. The assessment of PAH concentrations included the determination of medium-molecular-weight compounds from the US EPA list: fluoranthene—FLA, pyrene—PYR, benz(a)anthracene—BaA, and chrysene—CHR. The assessment was conducted using the GC-MS/MS technique. Three operationally defined fractions were investigated: total extractable PAHs (TE-PAHs) fraction, available/bioavailable PAHs (PB-PAHs) fraction, and nonavailable/residual PAHs (RE-PAHs) fraction, which was calculated as the difference between total and available PAHs. TE-PAHs were analyzed by dichloromethane extraction, while PB-PAHs were analyzed with a hydrophobic β-cyclodextrin solution. SOM was characterized by total organic carbon content (Turin method) and organic carbon of humic substances including FA, HA, HN (IHSS method). Concentrations of PAHs differed between soils from 193.5 to 3169.5 µg kg−1, 4.3 to 226.4 µg kg−1, and 148.6 to 3164.7 µg kg−1 for ∑4 TE-PAHs, ∑4 PB-PAHs, and ∑4 RE-PAHs, respectively. The ∑4 PB-PAHs fraction did not exceed 30% of ∑4 TE-PAHs. FLA was the most strongly bound in soil (highest content of RE-FLA), whereas PYR was the most available (highest content of PB-PYR). The soils were characterized by diversified total organic carbon (TOC) concentration (8.0–130.0 g kg−1) and individual SOM fractions (FA = 0.4–7.5 g kg−1, HA = 0.6–13.0 g kg−1, HN = 0.9–122.9 g kg−1). FA and HA as the labile fraction of SOM with short turnover time strongly positively influenced the potential ∑4 PAH availability (r = 0.56 and r = 0.52 for FA and HA, respectively). HN, which constitutes a stable fraction of organic matter with high hydrophobicity and poor degradability, was strongly correlated with ∑4 RE-PAHs (r = 0.75), affecting their persistence in soil.