Polysaccharides can form interfacial complexes with proteins to form emulsions with enhanced stability. We assessed the effect of adding gum guar or gum arabic to egg yolk/fish oil emulsions. The emulsions were produced using simple or high-pressure homogenization, stored for up to 10 days at 45 °C, and characterized for their particle size and distribution, viscosity, encapsulation efficiency, oxidative stability, and cytotoxicity. Emulsions containing gum guar and/or triglycerides had the highest viscosity. There was no significant difference in the encapsulation efficiency of emulsions regardless of the polysaccharide used. However, emulsions containing gum arabic displayed a bridging flocculation effect, resulting in less stability over time compared to those using gum guar. Emulsions produced using high-pressure homogenization displayed a narrower size distribution and higher stability. The formation of peroxides and propanal was lower in emulsions containing gum guar and was attributed to the surface oil. No significant toxicity toward Caco-2 cells was found from the emulsions over time. On the other hand, after 10 days of storage, nonencapsulated fish oil reduced the cell viability to about 80%. The results showed that gum guar can increase the particle stability of egg yolk/fish oil emulsions and decrease the oxidation rate of omega-3 fatty acids.