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Stearidonic acid (SDA; 18:4, n-3) is the delta 15-desaturase product of gamma linolenic acid (GLA; 18:3, n-6) and delta 6-desaturase product of alpha linolenic acid (ALA; 18:3, n-3). Construction of engineered oleaginous microbes have been attracting significant interest in producing SDA because of its nutritional value and pharmaceutical applications. <i>Mucor circinelloides</i> is a GLA producing filamentous fungus, which can be a useful tool to produce SDA. This study has, therefore, overexpressed the <i>delta-15 desaturase</i> (<i>D15D</i>) gene from <i>Mortierella alpina</i> in this fungus to construct a SDA-producing cell factory. To produce SDA in <i>M. circinelloides</i>, the homologous overexpression of <i>D15D</i> gene was analyzed. When the gene was overexpressed in <i>M. circinelloides</i> CBS 277.49, up to 5.0% SDA was accumulated in this strain. According to current knowledge, this is the first study describing the construction of a SDA-producing cell factory by overexpression of <i>D15D</i> gene in oleaginous fungus <i>M. circinelloides</i>. A new scope for further research has been established by this work to improve SDA production in this fungus, specifically in its high lipid-producing strain, WJ11.