A rapid method was developed to characterize the Pyrolytic Lignin (PL) fraction of flash pyrolysis bio-oils, based on size exclusion chromatography (SEC) coupled to differential refractive index (DRI) and multi-angle laser light scattering (MALS) detectors. Two beech wood bio-oils with different PL content were used in the study. The first was produced with a single-stage condensation system (BO), while the second was an organic fraction collected in the first stage of a two-stage condensation system (F1). PL was isolated from both the BO and F1 bio-oils by the water precipitation method. Our results suggested that quantification of the pyrolytic lignin fraction of biooils can be performed by the SEC-MALS-DRI method provided that the specific refractive index increment (dn/ dc) is known, and the integration interval is carefully chosen. Average molar mass (Mn) values for the BO and F1 samples were 580 ± 50 Da and 890 ± 50 Da, respectively. Our results indicated that the condensation system and the water precipitation method affect the average molar mass of isolated PL oligomers.