The concentration of nitrogen compounds in crude oils is relatively low, less than 2 wt %, but these compounds are detrimental to refining processes and the environment. In particular, they can form deposits, spoil fuels, and contribute to air pollution. They are potentially carcinogenic as well. Nitrogen compounds identified in refining processes come from the oil matrix, and it is desirable to know which nitrogen species are present in crude oil. However, the complexity of the crude oil makes it necessary to separate these compounds, and the conventional fractionation method is commonly used, albeit less efficiently in the separation of minority classes. Methods used to separate minority classes of nitrogen are time- and labor-intensive. We herein report a column chromatography separation method capable of separating minority classes, such as neutral and basic nitrogen compounds, using a silica gel modification with small quantities of crude oil (similar to 50 mg). The method showed good reproducibility in triplicate tests, using seven selected oils with API gravity ranging from 14.8 to 34.4. By modifying the silica gel with boric acid, aromatic nitrogen compounds were isolated and analyzed by a comprehensive two-dimensional gas chromatography (GCxGC-qMS) and Fourier transform ion cyclotronic resonance mass spectrometry (FT-ICR MS). More saturated fractions were retained in the unmodified silica gel, while modified silica gel retained more aromatic and polar fractions. Carbazole and pyridine homologous series were fully separated and identified, obtaining high-quality mass spectra for the compounds under study.