Animal feeds contain a substantial number and diversity of microorganisms, and some of them have pathogenic potential. The objectives of this study were to investigate the effects of different doses of gamma (γ)-ray irradiation on the bacteria count in different types of feed and then to test the effect of γ-ray-irradiation-treated fishmeal on the gut health and growth performance of weaning piglets. In trial 1, three fishmeal samples, two feather meal samples, three meat meal samples, three soybean meal samples, and three vitamin complexes were treated with γ-ray irradiation doses of 0, 3, 6, or 9 kGy. The 6 and 9 kGy doses eliminated most of the bacteria in the feed but also resulted in a loss of vitamin C and B1. In trial 2, 96 weaning piglets were fed one of the following three diets with eight replicates (pens) per group over a 14-day period: (1) the control diet—the basal diet supplemented with 6% fishmeal with a low bacteria count (40 CFU/g) and no E. coli; (2) the fishmeal-contaminated diet (FM-contaminated) diet—the basal diet supplemented with 6% fishmeal with a high bacteria count (91,500 CFU/g) and E. coli contamination; and (3) the irradiated fishmeal (irradiated FM) diet—the basal diet supplemented with γ-ray-irradiation-treated E. coli-contaminated fishmeal. The piglets that received the FM-contaminated diet had significantly lower average daily gain and a greater diarrhea index compared to those fed the control diet, whereas γ-ray irradiation treatment abrogated the negative effect of the E. coli-contaminated fishmeal. Collectively, γ-ray irradiation at a dose of 6–9 kGy was sufficient to eliminate the microorganisms in the feed, thereby benefitting the growth performance and gut health of the weaning piglets.