A systematic study was undertaken to identify the species, characterize the pathogenicity, and assess the immunization of Eimeria bateri in Japanese quail (Coturnix coturnix japonica). In total, 107 Japanese quail farms were examined. The samples were processed and oocyst shape indices of sporulated oocysts were determined. Out of 107 examined farms, 34 (31.78%) farms were positive. Four Eimeria spp. were morphologically identified. For characterization of the pathogenicity, Japanese quail were orally inoculated with various doses of sporulated oocysts of Eimeria bateri. Weight gain, feed conversion ratio (FCR), mortality, severity of diarrhea, and intestinal lesion scores were examined. The birds inoculated with high doses displayed significantly lower weight gain and poorer FCR, increased mortality, and more intestinal and fecal lesions scores. To quantify the immunization of Japanese quail against coccidiosis, 2-day-old quail were orally inoculated with either 100 or 1,000 sporulated oocysts of E. bateri. At 30 days of age, the immunized and non-immunized challenged birds were orally inoculated with 1 × 105 sporulated oocysts of E. bateri. After challenge, birds immunized with 100 or 1,000 oocysts had better weight gain, FCR, minimal diarrhea, fewer intestinal lesions, and lesser oocyst production compared to non-immunized challenged birds. We concluded that vaccination is a viable method for controlling coccidiosis in Japanese quail.