This study performs a screening of potential Ionic Liquids (ILs) for the extraction of Docosahexaenoic Acid (DHA) compounds by the calculation of capacity values. For this purpose, a Conductor-Like Screening Model for Real Solvents (COSMO-RS) was employed to study the molecular structures of the ILs, and therefore, predict their extraction potential. The capacity values of 22 anions combined with 16 cations based ILs, were investigated to evaluate the effectiveness of ILs in the extraction of DHA. It was found that among the investigated ILs, a combination of tetramethyl ammonium with SO4 or Cl was the best fit for DHA extraction, followed by pyrrolidinium, imidazolium, pyridinium and piperidinium. Furthermore, it was observed that the extraction capacity and the selectivity of ILs decreased with an increase in alkyl chain length; therefore, ethyl chain-ILs, with the shortest chain lengths, were found to be most suitable for DHA extraction. The predicted results were validated through the experimentally calculated extraction yield of a DHA compound from Nannochloropsis sp. Microalgae. Five selected ILs, namely [EMIM][Cl], [BMIM][Cl], [TMAm][Cl], [EMPyr][Br] and [EMPyrro][Br], were selected from COSMO-RS for empirical extraction purposes, and the validation results pinpointed the good prediction capabilities of COSMO-RS. The findings in this study can simplify the process of selecting suitable ILs for DHA extraction and reduce the number of required empirical evaluations.