We investigated the effects of fucoxanthin isolated from the edible macroalga Dilophys fasciola on pathogenic microbes and probiotics in vitro and the antioxidant activity of fucoxanthin. The yield concentration of the obtained crude was 50.5% fucoxanthin. We found strong inhibition against Grampositive Staphylococcus aureus and Listeria monocytogenes, and lower inhibition against Gram-negative bacteria and fungi. The probiotic strains progressed between 1.2 and 1.67 log cycles at a concentration of 30 μg/mL. The antioxidant activity ranged between 54.76% and 88.36% at a concentration of 40 μg/mL. The 50% lethal dose of algal fucoxanthin was shown to be more than 2511.88 mg/kg. The production of stirred yoghurt incorporated with 20 mg and 30 mg of fucoxanthin per kilogram of milk was evaluated through chemical, microbiological, and sensory analyses during storage for 21 days and compared with control samples. The maximum growth for probiotics (Bifidobacterium bifidum and Lacticaseibacillus casei) was found on day 14, but more viability counts were detected in the treatment with 30 mg/kg. All treatments were free from mould and yeast counts up to 7 days, and the small numbers of mould, yeast, and psychrotrophic counts appeared first in control samples. Also, the highest dry matter content was observed for treatments with 30 mg/kg. Moreover, the protein, fat, and ash content of all treatments increased with a progressive cold storage period. Greater reductions in the pH were found in treatments than in the control, and were consistent with the development of acidity. During storage, the amount of crude fucoxanthin had no significant impact on the flavour, colour, or appearance scores.