Commercially available solid phase extraction (SPE) cartridges were combined with GC–MS for fast cleanup and fractionation of biodiesel/diesel samples in oil fingerprinting analysis. Several commercially available SPE cartridges (e.g., silica gel/cyanopropyl (SiO₂/C₃–CN) and extractable petroleum hydrocarbons (EPH) fractionation cartridges), were employed for the fractionation of biodiesel/diesel blends into aliphatic, aromatic hydrocarbons, and fatty acid methyl esters (FAMEs). The SiO₂/C₃–CN (1 g/0.5 g) SPE cartridge could not separate biodiesel from petroleum hydrocarbons effectively, however, the 5 g EPH SPE cartridge successfully separated blended samples into aliphatic, aromatic and FAME fractions by eluting with 15 mL of hexane, 15 mL of dichloromethylene (DCM)/hexane (1 : 1, v/v), and 18 mL of DCM, respectively. No cross-elution was observed among aliphatic, aromatic and FAME fractions when the loading mass of blends was less than 8 mg. The relative standard deviations (RSD) for five replicate SPE–GC–MS analyses of 5 mg of diesel blended with 20% biodiesel (volume/volume) and soybean oil ranged from 3.4% to 33.2%, 4.3% to 18.7% and 5.4% to 29.2% for selected alkane, polycyclic aromatic hydrocarbons (PAHs) and FAMEs, respectively. The final recovery rates of surrogates for aliphatic, aromatic and FAME fractions ranged from 82.5 to 91.1%. This developed method was successfully used for the fingerprinting analysis of three simulated blend samples. The concentration profiles of target compounds and the blended level are both comparable to those obtained by the conventional silica gel column–GC–MS method.