Inflammation is part of the host’s normal response to various harmful stimuli, including chemical exposure, tissue damage, infection, or contact with bacterial components, such as lipopolysaccharide (LPS); however, excessive inflammation leads to various acute and chronic human diseases. Macrophages contribute to the inflammatory process by secreting inflammatory mediators, such as prostaglandin E2 (PGE2) and nitric oxide (NO), as well as proinflammatory cytokines such as IL-1[Formula: see text], TNF-[Formula: see text] and IL-6 and the excess of these mediators can be harmful to tissues and organisms. The RAW 264.7 murine macrophage cell line treated with LPS is a commonly used in vitro model for assessing anti-inflammatory efficacy. The base of conventional inflammation therapy is the use of steroidal and nonsteroidal anti-inflammatory medications, both of which have significant adverse effects. Therefore, finding new sources of less hazardous treatments is imperative. The anti-inflammatory qualities of bioactive lipids from crude extracts of the green alga Cladophora were investigated using ethanol and hexane-ether as two distinct solvents. As a result, the total lipid concentration of the hexane-ether extraction was higher, so the unsaturated fatty acids (UFAs) were extracted from this sample by the methanol-solvent crystallization technique at low temperatures. The presence of various fatty acids and their percentage purity were determined by gas chromatography (GC). After the elimination of 49.11% of the saturated fatty acids, the spontaneous nanoemulsification approach was applied to improve the stability and functionalization of the fatty acids. The nanoemulsion particles’ size, distribution, and stability were evaluated using a Zetasizer system. The mean particle size and zeta potential value were 194.3 nm and −25.8 mV, respectively. Finally, the MTT (thiazolyl blue tetrazolium bromide) assay was used to determine the toxicity of the extracted bioactive lipids in the macrophage cell line RAW264.7 for 24 h, and the results showed an increase in the viability of cells treated with UFAs after encapsulation. The IC[Formula: see text] values calculated from the MTT assay results for each formulation and the anti-inflammatory effects of each formulation (at 1/3 IC[Formula: see text] value) were determined in LPS-stimulated RAW 264.7 macrophages by performing nitric oxide (NO) and cytokine enzyme-linked immunosorbent assays. Nanoemulsions of polyunsaturated fatty acids inhibited the production of NO and interleukin 6, which may be promising candidates for biological and medical applications to combat inflammation.