Extraction yields and fatty acid profiles from freeze-dried Chlorella vulgaris by microwave pretreatment followed by supercritical carbon dioxide (MW-SCCO 2) extraction were compared with those obtained by supercritical carbon dioxide extraction alone (SCCO 2). Work performed with pressure range of 20–28 Mpa and temperature interval of 40–70 °C, gave the highest extraction yield (w/w dry weight) at 28 MPa/40 °C. MW-SCCO 2 allowed to obtain the highest extraction yield (4.73%) compared to SCCO 2 extraction alone (1.81%). Qualitative and quantitative analyses of microalgae oil showed that palmitic, oleic, linoleic and α-linolenic acid were the most abundant identified fatty acids. Oils obtained by MW-SCCO 2 extraction had the highest concentrations of fatty acids compared to SCCO 2 extraction without pretreatment. Native form, and microwave pretreated and untreated microalgae were observed by scanning electronic microscopy (SEM). SEM micrographs of pretreated microalgae present tearing wall agglomerates. After SCCO 2 , microwave pretreated microalgae presented several micro cracks; while native form microalgae wall was slightly damaged.