This study evaluated the protective effects of Lactobacillus acidophilus and Enterococcus faecium administered either in ovo or via drinking water in broiler chickens experimentally challenged with Eimeria spp. A total of 360 fertile eggs were allocated to four groups: control (no injection), FTS (0.1 mL physiological saline), LI (in ovo Lactobacillus acidophilus, 4 × 106 CFU per egg in 0.1 mL physiological saline), and EI (in ovo Enterococcus faecium, 2.5 × 106 CFU per egg in 0.1 mL physiological saline). Following hatch, chicks were assigned to six experimental groups (40 birds per group): NC (unchallenged, no probiotics), PC (Eimeria-challenged, no probiotics), LI (in ovo L. acidophilus), LW (L. acidophilus via drinking water), EI (in ovo E. faecium), and EW (E. faecium via drinking water). All groups except NC were orally challenged on day 10 with a live Eimeria vaccine administered at 50 times the recommended protective dose. Probiotic supplementation did not significantly affect growth performance parameters. However, all probiotic-treated groups exhibited significantly reduced fecal oocyst shedding and lower intestinal lesion scores compared with the challenged control group, indicating attenuation of Eimeria-associated intestinal pathology. Across the evaluated outcomes, E. faecium, particularly when administered via drinking water, exhibited the most consistent protective effects on lesion severity and oocyst shedding, without implying uniform statistical superiority across all comparisons. Cecal populations of Lactobacillus spp. and Enterococcus spp. were affected by probiotic strain and administration route, with higher counts observed in Enterococcus-supplemented birds. At day 21 post-challenge, probiotic supplementation was associated with enhanced antioxidant status, as reflected by increased activities of superoxide dismutase and catalase, and with modulation of systemic immune responses indicated by altered circulating concentrations of TNF-α, IL-6, and IL-10, with more pronounced and consistent changes observed in birds receiving probiotics via drinking water. In conclusion, probiotic supplementation reduced intestinal lesions and oocyst shedding while modulating antioxidant and immune responses during Eimeria infection. These findings suggest that E. faecium, particularly via drinking water, may support gut health and improve resilience against coccidiosis in broiler chickens.