Digital livestock system through convergence of livestock production and information and communication technology (ICT) is being applied to livestock farms to improve animal behavior and welfare, production, and quality of animal food. In previously study, we noted that the egg production were greatly enhanced in laying hens using digital livestock system. The present study investigated effects of a digital livestock system on fatty acid profiles and cholesterol of eggs, animal behavior, and welfare of laying hens. A total of 300 laying hens (Hy-Line Brown) at 48 weeks old were divided into two treatment groups: conventional livestock system (CON) and digital livestock system (DLS) in a randomized complete block design for 10 weeks. Drinking, feather squatting, eating, moving, preening, and resting scores as behavior indicators of laying hens were significantly improved in the DLS group than in the CON group (all P < 0.05). Animal welfare scores such as appearance, feather condition, body condition, and health of laying hens were significantly higher in the DLS group than in the CON group (P < 0.05). Contents of oleic acid and unsaturated fatty acid of eggs were significantly increased in the DLS group compared to the CON group (P < 0.05). However, content of saturated fatty acid and n-6/n-3 fatty acid ratio of eggs of the DLS group were significantly lower than those in the CON group (P < 0.05). These results indicate that the digital livestock system can be used as a future livestock farming algorithm to significantly improve egg fatty acid profile, animal behavior, and welfare in laying hens.