Mycotoxins contaminate cereal grains worldwide, and their presence in pet food has been a potential health threat to companion animals. Aflatoxins, ochratoxin A, and Fusarium mycotoxins have been found in both raw ingredients and final products of pet food around the globe. Aflatoxin, a hepatotoxin and carcinogen, has caused several food poisoning outbreaks in dogs, and aflatoxin content is regulated in pet food in many countries. Ochratoxin A and Fusarium mycotoxins including trichothecenes, zearalenone, and fumonisins may have chronic effects on the health of companion animals. Grain processing, sampling error, analytical methods, conjugated mycotoxins, storage conditions, and synergistic interactions are common challenges faced by the pet food industry. Food-processing techniques such as sieving, washing, pearling, ozonation, and acid-based mold inhibition reduce the mycotoxin content of cereal grains. Dietary supplementation with large neutral amino acids, antioxidants, and omega-3 polysaturated fatty acids as well as inclusion of mycotoxin-sequestering agents and detoxifying microbes may ameliorate the harmful effects of mycotoxins in contaminated pet food.