Pyrolysis oil and upgraded products are promising energy carriers. Characterisation of the oils is hampered due to the presence of a large number of components (>400) belonging to a broad variety of chemical compound classes (i.e., acids, aldehydes, ketones). In this study, a comparison of the capabilities of 2D-GC–FID and GC–MS to determine the molecular composition of these oils is made. As such, it represents a chromatographic study for a real application in green catalytic technology. Split-injection of the oil samples, diluted in tetrahydrofuran (THF), was applied without any sample pre-treatment. GC–MS application resulted in coelution, while 2D-GC showed significantly higher chromatographic resolution. Model compound mixtures were used for compound identification in the 2D-GC analysis while GC–MS was used to confirm the molecular structures. The combination of both 2D-GC–FID and GC–MS proved to be a useful method, without the requirement of a 2D-GC/TOF instrument. The technique was applied successfully to identify and quantify the main components in pyrolysis oil and upgraded pyrolysis oil made by hydrodeoxygenation (HDO) technology. Compared to GC–MS, 2D-GC–FID provides a fast overview of the various chemical compound classes present in the oils.