Food can contain unwanted compounds and need to be analyzed for compounds like carcinogenic polycyclic aromatic hydrocarbons to ensure consumer safety. The analytes need to be extracted from the sample matrix and cleaned-up to enable detection. However, established methods for clean-up are labor intensive and have a high expenditure on organic solvents. Here, we show a newly developed micro-solid-phase extraction cartridge method to automate the clean-up for analysis of polycyclic aromatic hydrocarbons in sunflower oil using gas chromatography with quadrupole-orbitrap mass spectrometry with a TriPlus autosampler. This automated micro-solid-phase extraction cartridge method needs only 4 μL of vegetable oil sample and requires only 360 μL acetonitrile for elution, and, therefore, it needs only small amounts of organic solvent. Two different micro-solid-phase extraction cartridge methods were developed, one using two commercially available cartridges with florisil and octadecylsilane/Z-Sep/CarbonX, and the other method using one commercially available cartridge with florisil followed by one self-made cartridge with octadecylsilane/Z-Sep. The latter method showed successful lipid removal and was further validated for 22 of 24 polycyclic aromatic hydrocarbon compounds in sunflower oil at a spiked level of 1090 μg/kg with recoveries ranging from 53 to 118% and relative standard deviation below 22%. This method shows promising short-time clean-up with low expenditure of solvents.