Lignans, such as flaxseed secoisolariciresinol diglucoside (SDG), have been implicated in the prevention of hormonally related cancers and other prevalent diseases. Lignans are typically extracted using organic solvents, which must then be removed from the extract. Supercritical carbon dioxide (SC-CO2) is a non-toxic, inexpensive solvent, which, when combined with polar modifiers, can be used to extract polar phenolic compounds, such as SDG. The effects of processing conditions and pre-treatment on the extraction of SDG using SC-CO2 were investigated. Extraction from defatted flaxseed was performed with SC-CO2 modified with ethanol at levels of 0, 10 and 20 mol% at different temperature (40, 50 and 60 °C) and pressure (35, 40 and 45 MPa) conditions. Extracts were analyzed using RP-HPLC. The condition (7.8 mol% ethanol, 45 MPa and 60 °C) which produced the maximum CO2 loading of SDG (0.49 μg/g CO2) was used for the pre-treatment study, in which flaxseed defatted with petroleum ether and SC-CO2, full-fat hulls, defatted hulls and pre-hydrolyzed flaxseed were used. Temperature, pressure and solvent modifier level had no significant effect (p > 0.05) on the SDG loading of CO2. However, pre-hydrolyzed seed resulted in a significantly (p ≤ 0.05) higher CO2 loading of SDG (3.8 μg/g CO2) compared to the other treatments studied. The yields obtained represented only a small fraction of the original lignan content (15 mg/g petroleum ether defatted flaxseed).