Soybean oil gums and soapstocks are important by-products that may potentially be contaminated by persistent organic pollutants (POP) such as polycyclic aromatic hydrocarbons (PAH) and phthalic acid esters (PAE), thus lowering the value when using them as starting materials to produce animal feed additives, food industry ingredients, and pharmaceutical products. In the present work, PAH and PAE distributions in these two types of by-products were detected using solvent extraction-solid phase extraction purification coupled with gas chromatography-mass spectrometry. Total PAH and PAE amounts in the soapstocks were significantly higher than those in the gums, thus indicating that neutralization showed much higher removal efficiency than degumming in terms of PAH and PAE eliminations. Meanwhile, the results proved that the concentrations of these two kinds of contaminants in the soybean oil gums and soapstocks were much higher than those in the soybean oils, suggesting that further investigations were needed and that the contents of PAH and PAE in soybean oil refining by-products should be carefully monitored and regulated.