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Whole sesame seeds (WSS) are rich in both linoleic acid (LA) and lignans. However, their impact on the innate immunity of goats is not well studied. Twenty-four goats were divided into three homogeneous sub-groups; comprise one control (CON) and two treated (WWS5 and WWS10). In the treated groups, WSS were incorporated in the concentrates of the CON at 5 (WSS5) and 10% (WSS10) respectively, by partial substitution of both soybean meal and corn grain. The expression levels of <i>MAPK1</i>, <i>IL6</i>, <i>TRIF</i>, <i>IFNG</i>, <i>TRAF3</i>, and <i>JUND</i> genes in the neutrophils of WSS10 fed goats were reduced significantly compared with the CON. The same was found for the expression levels of <i>IFNG</i> and <i>TRAF3</i> genes in the neutrophils of WSS5 fed goats. Both treated groups primarily affected the MYD88-independent pathway. The dietary supplementation of goats with WSS might be a good nutritional strategy to improve their innate immunity.